# HG changeset patch
# User peterjc
# Date 1348150396 14400
# Node ID 6ef523b390e0edeecac59632ad0d89cbf82f8333
# Parent  45ba7c750bc8be36f270934c681a089758e1c87e
Uploaded correct file.

diff -r 45ba7c750bc8 -r 6ef523b390e0 blast.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast.py	Thu Sep 20 10:13:16 2012 -0400
@@ -0,0 +1,124 @@
+"""
+BlastXml class
+"""
+
+from galaxy.datatypes.data import get_file_peek
+from galaxy.datatypes.data import Text
+from galaxy.datatypes.xml import GenericXml
+
+class BlastXml( GenericXml ):
+    """NCBI Blast XML Output data"""
+    file_ext = "blastxml"
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = 'NCBI Blast XML data'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def sniff( self, filename ):
+        """
+        Determines whether the file is blastxml
+        
+        >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
+        >>> BlastXml().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
+        >>> BlastXml().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'interval.interval' )
+        >>> BlastXml().sniff( fname )
+        False
+        """
+        #TODO - Use a context manager on Python 2.5+ to close handle
+        handle = open(filename)
+        line = handle.readline()
+        if line.strip() != '<?xml version="1.0"?>':
+            handle.close()
+            return False
+        line = handle.readline()
+        if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
+                                '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
+            handle.close()
+            return False
+        line = handle.readline()
+        if line.strip() != '<BlastOutput>':
+            handle.close()
+            return False
+        handle.close()
+        return True
+    
+    def merge(split_files, output_file):
+        """Merging multiple XML files is non-trivial and must be done in subclasses."""
+        if len(split_files) == 1:
+            #For one file only, use base class method (move/copy)
+            return Text.merge(split_files, output_file)
+        out = open(output_file, "w")
+        h = None
+        for f in split_files:
+            h = open(f)
+            body = False
+            header = h.readline()
+            if not header:
+                out.close()
+                h.close()
+                raise ValueError("BLAST XML file %s was empty" % f)
+            if header.strip() != '<?xml version="1.0"?>':
+                out.write(header) #for diagnosis
+                out.close()
+                h.close()
+                raise ValueError("%s is not an XML file!" % f)
+            line = h.readline()
+            header += line
+            if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
+                                    '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
+                out.write(header) #for diagnosis
+                out.close()
+                h.close()
+                raise ValueError("%s is not a BLAST XML file!" % f)
+            while True:
+                line = h.readline()
+                if not line:
+                    out.write(header) #for diagnosis
+                    out.close()
+                    h.close()
+                    raise ValueError("BLAST XML file %s ended prematurely" % f)
+                header += line
+                if "<Iteration>" in line:
+                    break
+                if len(header) > 10000:
+                    #Something has gone wrong, don't load too much into memory!
+                    #Write what we have to the merged file for diagnostics
+                    out.write(header)
+                    out.close()
+                    h.close()
+                    raise ValueError("BLAST XML file %s has too long a header!" % f)
+            if "<BlastOutput>" not in header:
+                out.close()
+                h.close()
+                raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
+            if f == split_files[0]:
+                out.write(header)
+                old_header = header
+            elif old_header[:300] != header[:300]:
+                #Enough to check <BlastOutput_program> and <BlastOutput_version> match
+                out.close()
+                h.close()
+                raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
+                                 % (split_files[0], f, old_header[:300], header[:300]))
+            else:
+                out.write("    <Iteration>\n")
+            for line in h:
+                if "</BlastOutput_iterations>" in line:
+                    break
+                #TODO - Increment <Iteration_iter-num> and if required automatic query names
+                #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
+                out.write(line)
+            h.close()
+        out.write("  </BlastOutput_iterations>\n")
+        out.write("</BlastOutput>\n")
+        out.close()
+    merge = staticmethod(merge)
+
diff -r 45ba7c750bc8 -r 6ef523b390e0 blast_datatypes.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_datatypes.txt	Thu Sep 20 10:13:16 2012 -0400
@@ -0,0 +1,98 @@
+Galaxy datatypes for NCBI BLAST+ suite
+======================================
+
+These Galaxy datatypes are copyright 2010-2012 by Peter Cock, The James Hutton
+Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+Note that these files (and the associated BLAST+ wrappers) were originally
+distributed as part of the main Galaxy repository, but as of August 2012 moved
+to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
+wrappers). My thanks to Dannon Baker from the Galaxy development team for his
+assistance with this.
+
+
+History
+=======
+
+These versions numbers match those for 'ncbi_blast_plus', but are not used
+explicitly in the datatypes themselves.
+
+v0.0.11 - Final revision as part of the Galaxy main repository, and the
+          first release via the Tool Shed
+v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
+
+
+Installation
+============
+
+Doing this automatically via the Galaxy Tool Shed is probably simplest.
+
+
+Manual Installation
+===================
+
+Normally you would install this via the Galaxy ToolShed, which would move
+the provided blast.py file into a suitable location and process the
+datatypes_conf.xml entry to be combined with your local configuration.
+
+However, if you really want to this should work for a manual install. Add
+the following line to the datatypes_conf.xml file in the Galaxy main folder:
+
+   <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
+
+Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
+the blast.py file provided in this tar-ball.  Finally add 'import blast' near
+the start of file lib/galaxy/datatypes/registry.py (after the other import
+lines).
+
+
+Developers
+==========
+
+BLAST+ datatypes and wrappers, and other tools are being developed on the
+following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
+the following command from the Galaxy tools/ncbi_blast_plus folder:
+
+$ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py
+
+Check this worked:
+
+$ tar -tzf blast_datatypes.tar.gz
+blast_datatypes.txt
+datatypes_conf.xml
+blast.py
+
+Note that the placement of these three files under tools/ncbi_blast_plus is
+arbitrary - this just puts them next to the tool wrappers which use them.
+
+For development, rather than having a local ToolShed running, I currently
+use a symlink from lib/galaxy/datatypes/blast.py to the actual file
+tools/ncbi_blast_plus/blast.py as described above.
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
+NOTE: This is the licence for the Galaxy BLAST datatypes  only. BLAST+
+and associated data files are available and licenced separately.
diff -r 45ba7c750bc8 -r 6ef523b390e0 datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Thu Sep 20 10:13:16 2012 -0400
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="blast.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
+    </registration>
+    <sniffers>
+        <sniffer type="galaxy.datatypes.blast:BlastXml"/>
+    </sniffers>
+</datatypes>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_four_human_vs_rhodopsin.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	96.55	348	12	0	1	348	1	348	0.0	 701
-sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU	84.80	342	51	1	1	341	1	342	0.0	 619
-sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1|	94.82	328	17	0	11	338	1	328	0.0	 653
-sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1|	94.82	328	17	0	11	338	1	328	0.0	 631
-sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A	93.10	348	23	1	1	348	1	347	0.0	 673
-sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	3e-176	 599
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_four_human_vs_rhodopsin.xml
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,646 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.25+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>
-  <BlastOutput_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
-  <BlastOutput_query-len>406</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM62</Parameters_matrix>
-      <Parameters_expect>1e-08</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|57163783|ref|NP_001009242.1|</Hit_id>
-          <Hit_def>rhodopsin [Felis catus]</Hit_def>
-          <Hit_accession>NP_001009242</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>701.049065538619</Hsp_bit-score>
-              <Hsp_score>1808</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-          <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-          <Hit_accession>P56514</Hit_accession>
-          <Hit_len>354</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>619.001555868222</Hsp_bit-score>
-              <Hsp_score>1595</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>342</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>290</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id>
-          <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def>
-          <Hit_accession>ADB45242</Hit_accession>
-          <Hit_len>328</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>653.284318124867</Hsp_bit-score>
-              <Hsp_score>1684</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>338</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>328</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>311</Hsp_identity>
-              <Hsp_positive>321</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>328</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id>
-          <Hit_def>rhodopsin [Myotis pilosus]</Hit_def>
-          <Hit_accession>ADB45229</Hit_accession>
-          <Hit_len>328</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>631.327942297578</Hsp_bit-score>
-              <Hsp_score>1627</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>338</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>328</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>311</Hsp_identity>
-              <Hsp_positive>323</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>328</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|223523|prf||0811197A</Hit_id>
-          <Hit_def>rhodopsin [Bos taurus]</Hit_def>
-          <Hit_accession>0811197A</Hit_accession>
-          <Hit_len>347</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>673.314696072569</Hsp_bit-score>
-              <Hsp_score>1736</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>347</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>324</Hsp_identity>
-              <Hsp_positive>336</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>
-          <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>
-          <Hit_accession>BAB21486</Hit_accession>
-          <Hit_len>354</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>599.356377496438</Hsp_bit-score>
-              <Hsp_score>1544</Hsp_score>
-              <Hsp_evalue>3.49521227372659e-176</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>342</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>281</Hsp_identity>
-              <Hsp_positive>314</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_four_human_vs_rhodopsin_converted.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin_converted.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	96.55	348	12	0	1	348	1	348	0.0	701
-sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU	84.80	342	51	1	1	341	1	342	0.0	619
-sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1|	94.82	328	17	0	11	338	1	328	0.0	653
-sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1|	94.82	328	17	0	11	338	1	328	0.0	631
-sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A	93.10	348	23	1	1	348	1	347	0.0	673
-sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	3e-176	599
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	96.55	348	12	0	1	348	1	348	0.0	701	gi|57163783|ref|NP_001009242.1|	1808	336	343	0	98.56	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	348
-sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU	84.80	342	51	1	1	341	1	342	0.0	619	gi|3024260|sp|P56514.1|OPSD_BUFBU	1595	290	322	1	94.15	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	354
-sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1|	94.82	328	17	0	11	338	1	328	0.0	653	gi|283855846|gb|ADB45242.1|	1684	311	321	0	97.87	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328
-sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1|	94.82	328	17	0	11	338	1	328	0.0	631	gi|283855823|gb|ADB45229.1|	1627	311	323	0	98.48	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328
-sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A	93.10	348	23	1	1	348	1	347	0.0	673	gi|223523|prf||0811197A	1736	324	336	1	96.55	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	347
-sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	3e-176	599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	96.55	348	12	0	1	348	1	348	0.0	 701	gi|57163783|ref|NP_001009242.1|	1808	336	343	0	98.56	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	348
-sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU	84.80	342	51	1	1	341	1	342	0.0	 619	gi|3024260|sp|P56514.1|OPSD_BUFBU	1595	290	322	1	94.15	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	354
-sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1|	94.82	328	17	0	11	338	1	328	0.0	 653	gi|283855846|gb|ADB45242.1|	1684	311	321	0	97.87	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328
-sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1|	94.82	328	17	0	11	338	1	328	0.0	 631	gi|283855823|gb|ADB45229.1|	1627	311	323	0	98.48	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328
-sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A	93.10	348	23	1	1	348	1	347	0.0	 673	gi|223523|prf||0811197A	1736	324	336	1	96.55	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	347
-sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	3e-176	 599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_human_vs_pdb_seg_no.xml
--- a/test-data/blastp_human_vs_pdb_seg_no.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,322 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.24+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db>/data/blastdb/pdbaa</BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
-  <BlastOutput_query-len>406</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM62</Parameters_matrix>
-      <Parameters_expect>1e-08</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|193885198|pdb|2R2J|A</Hit_id>
-          <Hit_def>Chain A, Crystal Structure Of Human Erp44</Hit_def>
-          <Hit_accession>2R2J_A</Hit_accession>
-          <Hit_len>382</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>768.073791748238</Hsp_bit-score>
-              <Hsp_score>1982</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>26</Hsp_query-from>
-              <Hsp_query-to>406</Hsp_query-to>
-              <Hsp_hit-from>2</Hsp_hit-from>
-              <Hsp_hit-to>382</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>370</Hsp_identity>
-              <Hsp_positive>372</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>381</Hsp_align-len>
-              <Hsp_qseq>PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL</Hsp_qseq>
-              <Hsp_hseq>PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL</Hsp_hseq>
-              <Hsp_midline>P+ +EITSLDTENIDEILNNADVALVNFYADWCRFSQ LHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNG   KREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPD VYLGA TNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFH KEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRH YVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|88192228|pdb|2B5E|A</Hit_id>
-          <Hit_def>Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase &gt;gi|206581884|pdb|3BOA|A Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase.</Hit_def>
-          <Hit_accession>2B5E_A</Hit_accession>
-          <Hit_len>504</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>95.130132620622</Hsp_bit-score>
-              <Hsp_score>235</Hsp_score>
-              <Hsp_evalue>4.15033135540548e-20</Hsp_evalue>
-              <Hsp_query-from>25</Hsp_query-from>
-              <Hsp_query-to>306</Hsp_query-to>
-              <Hsp_hit-from>10</Hsp_hit-from>
-              <Hsp_hit-to>283</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>73</Hsp_identity>
-              <Hsp_positive>133</Hsp_positive>
-              <Hsp_gaps>24</Hsp_gaps>
-              <Hsp_align-len>290</Hsp_align-len>
-              <Hsp_qseq>TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH</Hsp_qseq>
-              <Hsp_hseq>APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH</Hsp_hseq>
-              <Hsp_midline> P  + +  L T++ +E + + D+ L  F+A WC   + + P + +A++ + E+      +  A++DC ++ D+   + I  +P+LK+F+N  +    +Y G R+ +A+  ++ +Q    +  + DL      +     +I    + D+D    F  +AN   +D  F+SA          + D+    IY P     P +VY G    + + DV   W+Q + +P   EI      +  E GLP   LF+   D E LE ++          +G +NF+  D  KF RH</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>49615</Statistics_db-num>
-          <Statistics_db-len>11554246</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>2039204827</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|73536291|pdb|2BUJ|A</Hit_id>
-          <Hit_def>Chain A, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine &gt;gi|73536292|pdb|2BUJ|B Chain B, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine</Hit_def>
-          <Hit_accession>2BUJ_A</Hit_accession>
-          <Hit_len>317</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>105.530521170391</Hsp_bit-score>
-              <Hsp_score>262</Hsp_score>
-              <Hsp_evalue>1.04156432658542e-22</Hsp_evalue>
-              <Hsp_query-from>40</Hsp_query-from>
-              <Hsp_query-to>308</Hsp_query-to>
-              <Hsp_hit-from>21</Hsp_hit-from>
-              <Hsp_hit-to>294</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>82</Hsp_identity>
-              <Hsp_positive>130</Hsp_positive>
-              <Hsp_gaps>15</Hsp_gaps>
-              <Hsp_align-len>279</Hsp_align-len>
-              <Hsp_qseq>GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI</Hsp_qseq>
-              <Hsp_hseq>GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI</Hsp_hseq>
-              <Hsp_midline>G  V    +H + +++ L EGGFS V LV   H G   ALKR+  +   D    +RE   M  L  H NI+  +   +        E  +L+ + + G + N++ +    G   TE ++L +    C  +  +H       HRDLK  NILL D G  VL D GS     ++ +       +++   +  T+SYRAPE+ ++     I  + D+W+LGC+LY + F   P+      G+S         +IP + R+S  +  L+  M+  DP  RP I</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|270346335|pdb|2WQM|A</Hit_id>
-          <Hit_def>Chain A, Structure Of Apo Human Nek7 &gt;gi|270346336|pdb|2WQN|A Chain A, Structure Of Adp-Bound Human Nek7</Hit_def>
-          <Hit_accession>2WQM_A</Hit_accession>
-          <Hit_len>310</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>86.2705423745229</Hsp_bit-score>
-              <Hsp_score>212</Hsp_score>
-              <Hsp_evalue>6.48475818195287e-17</Hsp_evalue>
-              <Hsp_query-from>53</Hsp_query-from>
-              <Hsp_query-to>311</Hsp_query-to>
-              <Hsp_hit-from>36</Hsp_hit-from>
-              <Hsp_hit-to>288</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>74</Hsp_identity>
-              <Hsp_positive>129</Hsp_positive>
-              <Hsp_gaps>32</Hsp_gaps>
-              <Hsp_align-len>272</Hsp_align-len>
-              <Hsp_qseq>LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV</Hsp_qseq>
-              <Hsp_hseq>IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV</Hsp_hseq>
-              <Hsp_midline>+E+ +  G FS V+       G+  ALK++ + ++ D      C +EI ++K+L+ H N++ Y     + I DN  E+ I++E   AG +   +   KK +    E  V + F   C A+  +H  +  ++HRD+K  N+ +   G   L D G    +F + +    + +        T  Y +PE I+  G      K+DIW+LGCLLY++     PF   ++   ++C      ++    +  YS  +  L+   + PDPE RPD+  V</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>49615</Statistics_db-num>
-          <Statistics_db-len>11554246</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>6524204778</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|116667097|pdb|2DTG|E</Hit_id>
-          <Hit_def>Chain E, Insulin Receptor (Ir) Ectodomain In Complex With Fab&apos;s</Hit_def>
-          <Hit_accession>2DTG_E</Hit_accession>
-          <Hit_len>897</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>1846.24740474091</Hsp_bit-score>
-              <Hsp_score>4781</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>28</Hsp_query-from>
-              <Hsp_query-to>955</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>897</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>890</Hsp_identity>
-              <Hsp_positive>893</Hsp_positive>
-              <Hsp_gaps>31</Hsp_gaps>
-              <Hsp_align-len>928</Hsp_align-len>
-              <Hsp_qseq>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA</Hsp_qseq>
-              <Hsp_hseq>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA</Hsp_hseq>
-              <Hsp_midline>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDN+IVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV            PRPSRKRRSLGDVGN                     + EEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLC +RKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|114794482|pdb|2HR7|A</Hit_id>
-          <Hit_def>Chain A, Insulin Receptor (Domains 1-3) &gt;gi|114794483|pdb|2HR7|B Chain B, Insulin Receptor (Domains 1-3)</Hit_def>
-          <Hit_accession>2HR7_A</Hit_accession>
-          <Hit_len>486</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>1016.91271779085</Hsp_bit-score>
-              <Hsp_score>2628</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>28</Hsp_query-from>
-              <Hsp_query-to>512</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>485</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>483</Hsp_identity>
-              <Hsp_positive>485</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>485</Hsp_align-len>
-              <Hsp_qseq>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI</Hsp_qseq>
-              <Hsp_hseq>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI</Hsp_hseq>
-              <Hsp_midline>HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDN+IVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGD+ASCENELLKFSYIRTSFDKI</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>49615</Statistics_db-num>
-          <Statistics_db-len>11554246</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>7824126603</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|16975387|pdb|1JFP|A</Hit_id>
-          <Hit_def>Chain A, Structure Of Bovine Rhodopsin (Dark Adapted) &gt;gi|22219255|pdb|1LN6|A Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii) &gt;gi|157878065|pdb|1GZM|A Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form &gt;gi|157878066|pdb|1GZM|B Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form &gt;gi|157878298|pdb|1HZX|A Chain A, Crystal Structure Of Bovine Rhodopsin &gt;gi|157878299|pdb|1HZX|B Chain B, Crystal Structure Of Bovine Rhodopsin &gt;gi|157878979|pdb|1L9H|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution &gt;gi|157878980|pdb|1L9H|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution &gt;gi|157880263|pdb|1U19|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution &gt;gi|157880264|pdb|1U19|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution &gt;gi|157883606|pdb|2G87|A Chain A, Crystallographic Model Of Bathorhodopsin &gt;gi|157883607|pdb|2G87|B Chain B, Crystallographic Model Of Bathorhodopsin &gt;gi|157883830|pdb|2HPY|A Chain A, Crystallographic Model Of Lumirhodopsin &gt;gi|157883831|pdb|2HPY|B Chain B, Crystallographic Model Of Lumirhodopsin &gt;gi|157883860|pdb|2I35|A Chain A, Crystal Structure Of Rhombohedral Crystal Form Of Ground- State Rhodopsin &gt;gi|157883861|pdb|2I36|A Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin &gt;gi|157883862|pdb|2I36|B Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin &gt;gi|157883863|pdb|2I36|C Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin &gt;gi|157883864|pdb|2I37|A Chain A, Crystal Structure Of A Photoactivated Rhodopsin &gt;gi|157883865|pdb|2I37|B Chain B, Crystal Structure Of A Photoactivated Rhodopsin &gt;gi|157883866|pdb|2I37|C Chain C, Crystal Structure Of A Photoactivated Rhodopsin &gt;gi|159795066|pdb|2PED|A Chain A, Crystallographic Model Of 9-Cis-Rhodopsin &gt;gi|159795067|pdb|2PED|B Chain B, Crystallographic Model Of 9-Cis-Rhodopsin &gt;gi|192988480|pdb|3CAP|A Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State &gt;gi|192988481|pdb|3CAP|B Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State &gt;gi|195927457|pdb|3C9L|A Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form &gt;gi|197107530|pdb|1F88|A Chain A, Crystal Structure Of Bovine Rhodopsin &gt;gi|197107531|pdb|1F88|B Chain B, Crystal Structure Of Bovine Rhodopsin &gt;gi|206582030|pdb|3DQB|A Chain A, Crystal Structure Of The Active G-Protein-Coupled Receptor Opsin In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin</Hit_def>
-          <Hit_accession>1JFP_A</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>681.018687590916</Hsp_bit-score>
-              <Hsp_score>1756</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>325</Hsp_identity>
-              <Hsp_positive>337</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|195927458|pdb|3C9M|A</Hit_id>
-          <Hit_def>Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form</Hit_def>
-          <Hit_accession>3C9M_A</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>674.085095224404</Hsp_bit-score>
-              <Hsp_score>1738</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>324</Hsp_identity>
-              <Hsp_positive>335</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>M GTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>49615</Statistics_db-num>
-          <Statistics_db-len>11554246</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>1672994000</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular
--- a/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-sp|Q9BS26|ERP44_HUMAN	gi|193885198|pdb|2R2J|A	97.11	381	11	0	26	406	2	382	0.0	768	gi|193885198|pdb|2R2J|A	1982	370	372	0	97.64	1	1	PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL	PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL	406	382
-sp|Q9BS26|ERP44_HUMAN	gi|88192228|pdb|2B5E|A	25.17	290	193	8	25	306	10	283	4e-20	95.1	gi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A	235	73	133	24	45.86	1	1	TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH	APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH	406	504
-sp|Q9NSY1|BMP2K_HUMAN	gi|73536291|pdb|2BUJ|A	29.39	279	182	8	40	308	21	294	1e-22	105	gi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B	262	82	130	15	46.59	1	1	GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI	GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI	1161	317
-sp|Q9NSY1|BMP2K_HUMAN	gi|270346335|pdb|2WQM|A	27.21	272	166	12	53	311	36	288	6e-17	86.3	gi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A	212	74	129	32	47.43	1	1	LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV	IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV	1161	310
-sp|P06213|INSR_HUMAN	gi|116667097|pdb|2DTG|E	95.91	928	7	2	28	955	1	897	0.0	1846	gi|116667097|pdb|2DTG|E	4781	890	893	31	96.23	1	1	HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA	HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA	1382	897
-sp|P06213|INSR_HUMAN	gi|114794482|pdb|2HR7|A	99.59	485	2	0	28	512	1	485	0.0	1016	gi|114794482|pdb|2HR7|A;gi|114794483|pdb|2HR7|B	2628	483	485	0	100.00	1	1	HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI	HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI	1382	486
-sp|P08100|OPSD_HUMAN	gi|16975387|pdb|1JFP|A	93.39	348	23	0	1	348	1	348	0.0	681	gi|16975387|pdb|1JFP|A;gi|22219255|pdb|1LN6|A;gi|157878065|pdb|1GZM|A;gi|157878066|pdb|1GZM|B;gi|157878298|pdb|1HZX|A;gi|157878299|pdb|1HZX|B;gi|157878979|pdb|1L9H|A;gi|157878980|pdb|1L9H|B;gi|157880263|pdb|1U19|A;gi|157880264|pdb|1U19|B;gi|157883606|pdb|2G87|A;gi|157883607|pdb|2G87|B;gi|157883830|pdb|2HPY|A;gi|157883831|pdb|2HPY|B;gi|157883860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A	1756	325	337	0	96.84	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	348
-sp|P08100|OPSD_HUMAN	gi|195927458|pdb|3C9M|A	93.10	348	24	0	1	348	1	348	0.0	674	gi|195927458|pdb|3C9M|A	1738	324	335	0	96.26	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	348
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular
--- a/test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-sp|Q9BS26|ERP44_HUMAN	gi|193885198|pdb|2R2J|A	97.11	381	11	0	26	406	2	382	0.0	768
-sp|Q9BS26|ERP44_HUMAN	gi|88192228|pdb|2B5E|A	25.17	290	193	8	25	306	10	283	4e-20	95.1
-sp|Q9NSY1|BMP2K_HUMAN	gi|73536291|pdb|2BUJ|A	29.39	279	182	8	40	308	21	294	1e-22	105
-sp|Q9NSY1|BMP2K_HUMAN	gi|270346335|pdb|2WQM|A	27.21	272	166	12	53	311	36	288	6e-17	86.3
-sp|P06213|INSR_HUMAN	gi|116667097|pdb|2DTG|E	95.91	928	7	2	28	955	1	897	0.0	1846
-sp|P06213|INSR_HUMAN	gi|114794482|pdb|2HR7|A	99.59	485	2	0	28	512	1	485	0.0	1016
-sp|P08100|OPSD_HUMAN	gi|16975387|pdb|1JFP|A	93.39	348	23	0	1	348	1	348	0.0	681
-sp|P08100|OPSD_HUMAN	gi|195927458|pdb|3C9M|A	93.10	348	24	0	1	348	1	348	0.0	674
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_rhodopsin_vs_four_human.tabular
--- a/test-data/blastp_rhodopsin_vs_four_human.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-gi|57163783|ref|NP_001009242.1|	sp|P08100|OPSD_HUMAN	96.55	348	12	0	1	348	1	348	0.0	 679
-gi|3024260|sp|P56514.1|OPSD_BUFBU	sp|P08100|OPSD_HUMAN	83.33	354	53	2	1	354	1	348	6e-178	 605
-gi|283855846|gb|ADB45242.1|	sp|P08100|OPSD_HUMAN	94.82	328	17	0	1	328	11	338	0.0	 630
-gi|283855823|gb|ADB45229.1|	sp|P08100|OPSD_HUMAN	94.82	328	17	0	1	328	11	338	0.0	 630
-gi|223523|prf||0811197A	sp|P08100|OPSD_HUMAN	93.10	348	23	1	1	347	1	348	0.0	 651
-gi|12583665|dbj|BAB21486.1|	sp|P08100|OPSD_HUMAN	81.09	349	65	1	1	349	1	348	2e-172	 587
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_sample.xml
--- a/test-data/blastp_sample.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,293 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.24+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db>nr</BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>Sample</BlastOutput_query-def>
-  <BlastOutput_query-len>516</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM62</Parameters_matrix>
-      <Parameters_expect>1e-30</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>Sample</Iteration_query-def>
-      <Iteration_query-len>516</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|119953746|ref|YP_950551.1|</Hit_id>
-          <Hit_def>tail tape measure protein [Streptococcus phage SMP] &gt;gi|118430558|gb|ABK91882.1| tail tape measure protein [Streptococcus suis phage SMP]</Hit_def>
-          <Hit_accession>YP_950551</Hit_accession>
-          <Hit_len>659</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>949.117592429394</Hsp_bit-score>
-              <Hsp_score>2452</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>516</Hsp_query-to>
-              <Hsp_hit-from>27</Hsp_hit-from>
-              <Hsp_hit-to>542</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>500</Hsp_identity>
-              <Hsp_positive>500</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>516</Hsp_align-len>
-              <Hsp_qseq>FHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
-              <Hsp_hseq>FHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_hseq>
-              <Hsp_midline>FHLLNSGGSALSVMFAKLVGIIAGISAPIW                YNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|148986157|ref|ZP_01819143.1|</Hit_id>
-          <Hit_def>unknown phage protein [Streptococcus pneumoniae SP3-BS71] &gt;gi|147921871|gb|EDK72998.1| unknown phage protein [Streptococcus pneumoniae SP3-BS71]</Hit_def>
-          <Hit_accession>ZP_01819143</Hit_accession>
-          <Hit_len>1031</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>174.481245259597</Hsp_bit-score>
-              <Hsp_score>441</Hsp_score>
-              <Hsp_evalue>1.54640812741294e-41</Hsp_evalue>
-              <Hsp_query-from>49</Hsp_query-from>
-              <Hsp_query-to>300</Hsp_query-to>
-              <Hsp_hit-from>679</Hsp_hit-from>
-              <Hsp_hit-to>897</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>104</Hsp_identity>
-              <Hsp_positive>148</Hsp_positive>
-              <Hsp_gaps>33</Hsp_gaps>
-              <Hsp_align-len>252</Hsp_align-len>
-              <Hsp_qseq>TNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
-              <Hsp_hseq>TNEGFRDAVTTVWNAILEVINAVVSEISNFVMSIFGTVVTWWTENQELIRTSAETVWNAIYTVISTILDILGPLLQAGWDNIQLIITTTWEIIKIVVETAINVVLGVIQAVMQIITGDWSGAWETIKGVFSTVWQAIQSIVQT-------IFSAIQSYISNILNGISGT----VSNIWNSIKDTVSN----------------------VLNAISSTVSSVWEGIKSTISSAINGARDAVSSAIEAIKGLFN</Hsp_hseq>
-              <Hsp_midline>TNE FR  V   W AI   I+  V  + +FVM ++G +V WW ENQELIR +AETVWNAI TV+ T++  L P++Q  WD I  ++TT   +IK VV+T + VVLG+I+AVMQ+I GDWSGAWET+KGV  T+W+ I+S+VQ        IF    +++ +I + + GT    V  IW+ IK TVSN                      V NAIS+  S++W  I +T+ S +      + + +E IK +++</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>3</Hit_num>
-          <Hit_id>gi|77411259|ref|ZP_00787609.1|</Hit_id>
-          <Hit_def>tail tape meausure protein [Streptococcus agalactiae CJB111] &gt;gi|77162685|gb|EAO73646.1| tail tape meausure protein [Streptococcus agalactiae CJB111]</Hit_def>
-          <Hit_accession>ZP_00787609</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>165.621655013498</Hsp_bit-score>
-              <Hsp_score>418</Hsp_score>
-              <Hsp_evalue>7.61538823982138e-39</Hsp_evalue>
-              <Hsp_query-from>50</Hsp_query-from>
-              <Hsp_query-to>310</Hsp_query-to>
-              <Hsp_hit-from>655</Hsp_hit-from>
-              <Hsp_hit-to>904</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>107</Hsp_identity>
-              <Hsp_positive>158</Hsp_positive>
-              <Hsp_gaps>11</Hsp_gaps>
-              <Hsp_align-len>261</Hsp_align-len>
-              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF</Hsp_qseq>
-              <Hsp_hseq>HEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNAINGAKNAVSSAINAIKNLF</Hsp_hseq>
-              <Hsp_midline>+E FRT V   W AI + +S  ++ + SFVM +WG +  WW ENQ+LI   A TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q       F+ + W+ + GT+  ++    + IK+ VSN   ++   I +I++SI +T  +VWN +    S + + IS TV SV   +   I   +   K   S+A   IK +F</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>4</Hit_num>
-          <Hit_id>gi|76786754|ref|YP_329383.1|</Hit_id>
-          <Hit_def>prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909] &gt;gi|76561811|gb|ABA44395.1| prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909]</Hit_def>
-          <Hit_accession>YP_329383</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>159.073262222903</Hsp_bit-score>
-              <Hsp_score>401</Hsp_score>
-              <Hsp_evalue>6.55719737745379e-37</Hsp_evalue>
-              <Hsp_query-from>50</Hsp_query-from>
-              <Hsp_query-to>310</Hsp_query-to>
-              <Hsp_hit-from>655</Hsp_hit-from>
-              <Hsp_hit-to>904</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>103</Hsp_identity>
-              <Hsp_positive>156</Hsp_positive>
-              <Hsp_gaps>11</Hsp_gaps>
-              <Hsp_align-len>261</Hsp_align-len>
-              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF</Hsp_qseq>
-              <Hsp_hseq>HEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAIKNLF</Hsp_hseq>
-              <Hsp_midline>+E FRT V   W AI + ++  ++ + SFVM +WG ++ WW ENQ+LI     TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q       F+ + W+ + GT+  ++    + IK  VSN    +   I +I++SI +T  ++WN +    S + + IS+TV  V   +   I   +   K   S+A   IK +F</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>5</Hit_num>
-          <Hit_id>gi|153811333|ref|ZP_01964001.1|</Hit_id>
-          <Hit_def>hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] &gt;gi|149832460|gb|EDM87544.1| hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174]</Hit_def>
-          <Hit_accession>ZP_01964001</Hit_accession>
-          <Hit_len>1228</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>157.147264343316</Hsp_bit-score>
-              <Hsp_score>396</Hsp_score>
-              <Hsp_evalue>2.33083876931167e-36</Hsp_evalue>
-              <Hsp_query-from>3</Hsp_query-from>
-              <Hsp_query-to>516</Hsp_query-to>
-              <Hsp_hit-from>573</Hsp_hit-from>
-              <Hsp_hit-to>1059</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>167</Hsp_identity>
-              <Hsp_positive>247</Hsp_positive>
-              <Hsp_gaps>113</Hsp_gaps>
-              <Hsp_align-len>557</Hsp_align-len>
-              <Hsp_qseq>LLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQV---AIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLI-----------KQAISNAWEIIKTKT-----------------------SEIWNAITTFLSGIWEGIKTAASTAWEWIKTT-ISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIEN-IKSTVSNGWNNL---VSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLI-NGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
-              <Hsp_hseq>LVKAGG--FSGVFTKALGLI---TSPAAIVVGVIAAITAVIIHLWNTNEDFRNTITAIWQKIKDAFTT---------------FAAGISERLSALGITFSDVTSAIKTIWDGFCNLLAPVLEAAFSTIAIALQTAFNVI-----------LGIWDVFSAVFSGDWSGAWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVF---LGWFGTNWETVWNGVKTFFEGIW--------NGISSFFEGI--------------WNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNA---IKTTVQTVF-NAVKTTVTTIWNAIKTGTSTAWN----AVKTAVTTPINAAKSAVTSAIN------GIKS</Hsp_hseq>
-              <Hsp_midline>L+ +GG   S +F K +G+I   ++P                  +NTNE+FR  + A W+ IK A +T                 A  +E    +  T   V +AI+T+ +     L P+++ A+  I   + T  NVI           LGI      + +GDWSGAWE +KG+  +IW+G+K        A+ G+  +F   L +  + W+TVW  +      IW        N I++ +E I              WN IST  + +W  I T V +  TT+   I T    +K V S  WE IK V    ++ IV +V   F+LI           +  I + WE IK+                         + +WNAI T  + +   IK+A  TAW ++K   ++ VM  I + I T WN IKT+ +  +N IKSA + AWN +K+++ T + N IK+ ++  WN +   V TV NA   I + V+T F NAV      I NAI  G     N     VK A    I+A   AV+ AI+      GIKS</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>6</Hit_num>
-          <Hit_id>gi|56962696|ref|YP_174422.1|</Hit_id>
-          <Hit_def>hypothetical protein ABC0922 [Bacillus clausii KSM-K16] &gt;gi|56908934|dbj|BAD63461.1| phage-related protein [Bacillus clausii KSM-K16]</Hit_def>
-          <Hit_accession>YP_174422</Hit_accession>
-          <Hit_len>593</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>146.746875793547</Hsp_bit-score>
-              <Hsp_score>369</Hsp_score>
-              <Hsp_evalue>3.12404663750498e-33</Hsp_evalue>
-              <Hsp_query-from>48</Hsp_query-from>
-              <Hsp_query-to>433</Hsp_query-to>
-              <Hsp_hit-from>123</Hsp_hit-from>
-              <Hsp_hit-to>465</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>112</Hsp_identity>
-              <Hsp_positive>187</Hsp_positive>
-              <Hsp_gaps>49</Hsp_gaps>
-              <Hsp_align-len>389</Hsp_align-len>
-              <Hsp_qseq>NTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGL---VQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN</Hsp_qseq>
-              <Hsp_hseq>QTNETFRNGVIQAWEAIKTTMETVVATIVTFVSEKLAQIKAFWDEHGAAVMQAVTNIFNGIKSIIEPVMNGILAIMQFVWPFIVSLIQMVWGNIQGVISGALNIIMGLVKAFAGLFTGDFS-----------LMWEGIKQLFSGALEAIWNVVQLLLFGR--LLKIASSLFTGLMGVFSKMWGAISNLFLTALNGIRSFFSTIFTPIQ-------NVVMTVMGFIRNAISTG----LTTASNVVQTVLTAIRTVFLTVFNAVRNV-----------VTTAISFVQNFISTGISAARTAVTSALNAIKTTFTTIFNAVRSSVTTAMTNIKTAISN-------GIQSAWQ----AVLNFVGRFREAGKNIVNSIAEGITSAIGAVKNAISN</Hsp_hseq>
-              <Hsp_midline> TNE FR  V  AWEAIK+ + T V  +V+FV +   Q+ A+W+E+   + Q    ++N I++++E VM  ++ I+Q  W  I++++  V   I+ V+   L +++G++KA   +  GD+S            +WEGIK L   A++ +   VQ+   G   L  I  +++  +M V   +W  I      A+  +      I T IQ       N + TV   I  AIST     LTT    +QT L  I+TV+   +  ++ V           VT     ++  IS      +T  +   NAI T  + I+  ++++ +TA   IKT ISN        I++AW     ++ N +   + A +N  N+I   I++AI  +K+ +SN</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>7</Hit_num>
-          <Hit_id>gi|50914476|ref|YP_060448.1|</Hit_id>
-          <Hit_def>unknown phage protein [Streptococcus pyogenes MGAS10394] &gt;gi|40218580|gb|AAR83234.1| prophage pi2 protein [Streptococcus pyogenes] &gt;gi|50261625|gb|AAT72393.1| unknown [Streptococcus pyogenes] &gt;gi|50903550|gb|AAT87265.1| unknown phage protein [Streptococcus pyogenes MGAS10394]</Hit_def>
-          <Hit_accession>YP_060448</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>146.36167621763</Hsp_bit-score>
-              <Hsp_score>368</Hsp_score>
-              <Hsp_evalue>4.74132513340056e-33</Hsp_evalue>
-              <Hsp_query-from>50</Hsp_query-from>
-              <Hsp_query-to>227</Hsp_query-to>
-              <Hsp_hit-from>655</Hsp_hit-from>
-              <Hsp_hit-to>832</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>78</Hsp_identity>
-              <Hsp_positive>112</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>178</Hsp_align-len>
-              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWD</Hsp_qseq>
-              <Hsp_hseq>NEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWN</Hsp_hseq>
-              <Hsp_midline>NE FRT V   W AI + IS  ++ + +F+M +WG +  WW ENQ LI+   ETVWNAI TV++TVM+ + P ++ AW  I  ++TT   +IKTVV+T + VVLGIIKA+MQ I GDWSGAWET+KGV   +W+ I+ +V   +  + Q        +K+ +  +   I  +V  IW+</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>8</Hit_num>
-          <Hit_id>gi|29374987|ref|NP_814140.1|</Hit_id>
-          <Hit_def>tail protein [Enterococcus faecalis V583] &gt;gi|29342445|gb|AAO80211.1| tail protein [Enterococcus faecalis V583]</Hit_def>
-          <Hit_accession>NP_814140</Hit_accession>
-          <Hit_len>1049</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>139.0428842752</Hsp_bit-score>
-              <Hsp_score>349</Hsp_score>
-              <Hsp_evalue>6.84844401007043e-31</Hsp_evalue>
-              <Hsp_query-from>73</Hsp_query-from>
-              <Hsp_query-to>482</Hsp_query-to>
-              <Hsp_hit-from>545</Hsp_hit-from>
-              <Hsp_hit-to>920</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>110</Hsp_identity>
-              <Hsp_positive>196</Hsp_positive>
-              <Hsp_gaps>78</Hsp_gaps>
-              <Hsp_align-len>432</Hsp_align-len>
-              <Hsp_qseq>EAVVSFVMDLWGQMVAWWNENQELIRQ-------TAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVL----NVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSIS-----------NALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGF</Hsp_qseq>
-              <Hsp_hseq>DSIVKTASGLKGSLVKTWNDITAKVSEIWKKFTDAGKKTFDGFKKTVENVFNGIKNFLQTVWNVIYAVVGAIIVNTINIWKGIFDG--------FKAYFQYL-------WDLIKAIATGVWEKIGDTVTGIINGFIGVIKGIFDAFKTFFQQIWDAVVYSVTIAWNGIKNTVTSVSTAIKNFVTPIFNAIKTTITNVFNAIKNTATNVWNAIKTTISNVVQTILNF---------------------------------VTPIFNTMKNTITNIFNAIRNTASSVWNSIKTTISNIVTSVKNTVINIFNALKNSITNIFNAIRNTASTVWNSIKSTVSNIVSATVNTVKNLFNGMKNTVSSIWDGVRNTISNVVNAVKNTISNVWGGITGTVSN----IFNGVKNAIDGPMNAAKNLVKNVV----DAIKGF</Hsp_hseq>
-              <Hsp_midline>+++V     L G +V  WN+    + +         +  ++  +  VE V   +   +QT W++I AVV  ++    N+ K + D          KA  Q +       W+ +K +A  +WE I   V   I+G + + +      K+ +  +W  ++  V   W+ IK TV++  TA+   +  I  +I+TT   V+NAI   A+N+W AI TT+ +V+ TI  +                                 VT  F+ +K  I+N +  I+   S +WN+I T +S I   +K      +  +K +I+N+   I++   T WN+IK+++S           N  N +K+   + W+ +++ IS  +  +K+T+SN W  +  TV+N    I + V+   D  +NAA+N + N +    D I GF</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>9</Hit_num>
-          <Hit_id>gi|163941333|ref|YP_001646217.1|</Hit_id>
-          <Hit_def>prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4] &gt;gi|163863530|gb|ABY44589.1| prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4]</Hit_def>
-          <Hit_accession>YP_001646217</Hit_accession>
-          <Hit_len>725</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>138.657684699283</Hsp_bit-score>
-              <Hsp_score>348</Hsp_score>
-              <Hsp_evalue>8.15996781441799e-31</Hsp_evalue>
-              <Hsp_query-from>61</Hsp_query-from>
-              <Hsp_query-to>480</Hsp_query-to>
-              <Hsp_hit-from>142</Hsp_hit-from>
-              <Hsp_hit-to>560</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>118</Hsp_identity>
-              <Hsp_positive>203</Hsp_positive>
-              <Hsp_gaps>29</Hsp_gaps>
-              <Hsp_align-len>434</Hsp_align-len>
-              <Hsp_qseq>WEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIK---AVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKT----VWS-------AAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLIN</Hsp_qseq>
-              <Hsp_hseq>WDAIKQWTIDAWNAIGEFLVGIWDGIVQWASEAWNSISESTSAVWNSIKEFLIGIWNGIVEFVVT-WGT--AILETYVGIWTSIFNFCMEIWNGIVEYLTSVLQGIATFFTEIWTSISTFFQEIWNGLVAFITPVLQGIADFFAM-----------IWNGISTVIQTVWNFITQYLQAIWTAILYFATPLFESIKNFISECWNKISSTTSLVWETIKNFLVSCWNGLVSFVTPIFEKIKSWIISVWDTISSATMAVWNAVKNFLQACWNGLVSIVTPIFDAIKNWIVNVWNAISSTTSAVWNAIKSYLSSLWNSIVSTASSIFNSIKSAISTVWNMISSASSSVWNGIKSTLSSIWNGIKSTASSVWNGLKDAIMTPVRWVTSAVSGAFNGMKSAVLGVWDGIKSGIRTAINGIIRIINKFI-DGFNTPAELLN</Hsp_hseq>
-              <Hsp_midline>W+AIK     A  A+  F++ +W  +V W +E    I ++   VWN+I+  +  +   ++  V T W    A++ T + +  ++ +  +++  GI++   +V+Q I   ++  W ++      IW G+ + +   + G+   F             +W  I  V+  +W++I   +    TA+      +  SI+      WN IS+  S +W  I   ++S    +  ++    E IK+    VW        A W  +K    A    +V +VT  FD IK  I N W  I + TS +WNAI ++LS +W  I + AS+ +  IK+ IS V   I S   + WN IK+++S+  N IKS A + WN +K AI T +  + S VS  +N + S V      I S +RT  +  +     FI +  +   +L+N</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>6589360</Statistics_db-num>
-          <Statistics_db-len>-2041834015</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>504129014857</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastp_sample_converted.tabular
--- a/test-data/blastp_sample_converted.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-Sample	gi|119953746|ref|YP_950551.1|	96.90	516	16	0	1	516	27	542	0.0	949
-Sample	gi|148986157|ref|ZP_01819143.1|	41.27	252	115	3	49	300	679	897	2e-41	174
-Sample	gi|77411259|ref|ZP_00787609.1|	41.00	261	143	2	50	310	655	904	8e-39	165
-Sample	gi|76786754|ref|YP_329383.1|	39.46	261	147	2	50	310	655	904	7e-37	159
-Sample	gi|153811333|ref|ZP_01964001.1|	29.98	557	277	18	3	516	573	1059	2e-36	157
-Sample	gi|56962696|ref|YP_174422.1|	28.79	389	228	8	48	433	123	465	3e-33	146
-Sample	gi|50914476|ref|YP_060448.1|	43.82	178	100	0	50	227	655	832	5e-33	146
-Sample	gi|29374987|ref|NP_814140.1|	25.46	432	244	8	73	482	545	920	7e-31	139
-Sample	gi|163941333|ref|YP_001646217.1|	27.19	434	287	7	61	480	142	560	8e-31	138
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_rhodopsin_vs_four_human.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-gi|57163782|ref|NM_001009242.1|	sp|P08100|OPSD_HUMAN	96.55	348	12	0	1	1044	1	348	0.0	 662
-gi|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	1e-168	 575
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.40	111	4	0	1	333	11	121	2e-62	 224
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.31	65	5	0	3174	3368	248	312	5e-34	 129
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.43	56	2	0	2855	3022	177	232	2e-31	 120
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	93.22	59	4	0	1404	1580	119	177	1e-30	 118
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.00	25	2	0	4222	4296	312	336	6e-12	56.2
-gi|283855822|gb|GQ290312.1|	sp|P08100|OPSD_HUMAN	95.09	326	16	0	1	978	11	336	2e-180	 613
-gi|18148870|dbj|AB062417.1|	sp|P08100|OPSD_HUMAN	93.39	348	23	0	1	1044	1	348	0.0	 641
-gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	6e-164	 559
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_rhodopsin_vs_four_human.xml
--- a/test-data/blastx_rhodopsin_vs_four_human.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,722 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastx</BlastOutput_program>
-  <BlastOutput_version>BLASTX 2.2.25+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</BlastOutput_query-def>
-  <BlastOutput_query-len>1047</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM62</Parameters_matrix>
-      <Parameters_expect>1e-10</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>L;</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>662.143908370966</Hsp_bit-score>
-              <Hsp_score>1707</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>1044</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>1</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def>
-      <Iteration_query-len>1574</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>32</Statistics_hsp-len>
-          <Statistics_eff-space>155472</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def>
-      <Iteration_query-len>1574</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>32</Statistics_hsp-len>
-          <Statistics_eff-space>155472</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def>
-      <Iteration_query-len>1574</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>32</Statistics_hsp-len>
-          <Statistics_eff-space>155472</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def>
-      <Iteration_query-len>1574</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>575.088804213644</Hsp_bit-score>
-              <Hsp_score>1481</Hsp_score>
-              <Hsp_evalue>1.31349806431671e-168</Hsp_evalue>
-              <Hsp_query-from>42</Hsp_query-from>
-              <Hsp_query-to>1037</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>332</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>283</Hsp_identity>
-              <Hsp_positive>315</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>332</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>32</Statistics_hsp-len>
-          <Statistics_eff-space>155472</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def>
-      <Iteration_query-len>4301</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>430746</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def>
-      <Iteration_query-len>4301</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>430746</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def>
-      <Iteration_query-len>4301</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>430746</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def>
-      <Iteration_query-len>4301</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>224.171990552935</Hsp_bit-score>
-              <Hsp_score>570</Hsp_score>
-              <Hsp_evalue>1.57574304751949e-62</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>333</Hsp_query-to>
-              <Hsp_hit-from>11</Hsp_hit-from>
-              <Hsp_hit-to>121</Hsp_hit-to>
-              <Hsp_query-frame>1</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>107</Hsp_identity>
-              <Hsp_positive>109</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>111</Hsp_align-len>
-              <Hsp_qseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
-              <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>129.412894877266</Hsp_bit-score>
-              <Hsp_score>324</Hsp_score>
-              <Hsp_evalue>5.28220874623366e-34</Hsp_evalue>
-              <Hsp_query-from>3174</Hsp_query-from>
-              <Hsp_query-to>3368</Hsp_query-to>
-              <Hsp_hit-from>248</Hsp_hit-from>
-              <Hsp_hit-to>312</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>60</Hsp_identity>
-              <Hsp_positive>64</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>65</Hsp_align-len>
-              <Hsp_qseq>KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_qseq>
-              <Hsp_hseq>KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_hseq>
-              <Hsp_midline>KEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>120.938504207085</Hsp_bit-score>
-              <Hsp_score>302</Hsp_score>
-              <Hsp_evalue>1.87871691987854e-31</Hsp_evalue>
-              <Hsp_query-from>2855</Hsp_query-from>
-              <Hsp_query-to>3022</Hsp_query-to>
-              <Hsp_hit-from>177</Hsp_hit-from>
-              <Hsp_hit-to>232</Hsp_hit-to>
-              <Hsp_query-frame>2</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>54</Hsp_identity>
-              <Hsp_positive>56</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>56</Hsp_align-len>
-              <Hsp_qseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE</Hsp_qseq>
-              <Hsp_hseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE</Hsp_hseq>
-              <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>118.242107175663</Hsp_bit-score>
-              <Hsp_score>295</Hsp_score>
-              <Hsp_evalue>1.21774886471054e-30</Hsp_evalue>
-              <Hsp_query-from>1404</Hsp_query-from>
-              <Hsp_query-to>1580</Hsp_query-to>
-              <Hsp_hit-from>119</Hsp_hit-from>
-              <Hsp_hit-to>177</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>55</Hsp_identity>
-              <Hsp_positive>56</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_qseq>
-              <Hsp_hseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_hseq>
-              <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>56.2249754529693</Hsp_bit-score>
-              <Hsp_score>134</Hsp_score>
-              <Hsp_evalue>5.68296036241677e-12</Hsp_evalue>
-              <Hsp_query-from>4222</Hsp_query-from>
-              <Hsp_query-to>4296</Hsp_query-to>
-              <Hsp_hit-from>312</Hsp_hit-from>
-              <Hsp_hit-to>336</Hsp_hit-to>
-              <Hsp_query-frame>1</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>23</Hsp_identity>
-              <Hsp_positive>24</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>25</Hsp_align-len>
-              <Hsp_qseq>QFRNCMLTTLCCGKNPLGDDEASTT</Hsp_qseq>
-              <Hsp_hseq>QFRNCMLTTICCGKNPLGDDEASAT</Hsp_hseq>
-              <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>430746</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def>
-      <Iteration_query-len>983</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>28</Statistics_hsp-len>
-          <Statistics_eff-space>95680</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def>
-      <Iteration_query-len>983</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>28</Statistics_hsp-len>
-          <Statistics_eff-space>95680</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def>
-      <Iteration_query-len>983</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>28</Statistics_hsp-len>
-          <Statistics_eff-space>95680</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def>
-      <Iteration_query-len>983</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>613.993961381297</Hsp_bit-score>
-              <Hsp_score>1582</Hsp_score>
-              <Hsp_evalue>1.57028732393616e-180</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>978</Hsp_query-to>
-              <Hsp_hit-from>11</Hsp_hit-from>
-              <Hsp_hit-to>336</Hsp_hit-to>
-              <Hsp_query-frame>1</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>310</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>326</Hsp_align-len>
-              <Hsp_qseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_qseq>
-              <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>28</Statistics_hsp-len>
-          <Statistics_eff-space>95680</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>Query_5</Iteration_query-ID>
-      <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>Query_5</Iteration_query-ID>
-      <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>Query_5</Iteration_query-ID>
-      <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>Query_5</Iteration_query-ID>
-      <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1047</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>641.728330847346</Hsp_bit-score>
-              <Hsp_score>1654</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>1044</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>1</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>325</Hsp_identity>
-              <Hsp_positive>337</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>102080</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>Query_6</Iteration_query-ID>
-      <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1344</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>31</Statistics_hsp-len>
-          <Statistics_eff-space>132189</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>Query_6</Iteration_query-ID>
-      <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1344</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>31</Statistics_hsp-len>
-          <Statistics_eff-space>132189</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>Query_6</Iteration_query-ID>
-      <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1344</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>31</Statistics_hsp-len>
-          <Statistics_eff-space>132189</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>Query_6</Iteration_query-ID>
-      <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>
-      <Iteration_query-len>1344</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>559.295621601033</Hsp_bit-score>
-              <Hsp_score>1440</Hsp_score>
-              <Hsp_evalue>6.32632556748138e-164</Hsp_evalue>
-              <Hsp_query-from>23</Hsp_query-from>
-              <Hsp_query-to>1018</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>332</Hsp_hit-to>
-              <Hsp_query-frame>2</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>272</Hsp_identity>
-              <Hsp_positive>307</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>332</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP  +++</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>31</Statistics_hsp-len>
-          <Statistics_eff-space>132189</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_rhodopsin_vs_four_human_converted.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-gi|57163782|ref|NM_001009242.1|	sp|P08100|OPSD_HUMAN	96.55	348	12	0	1	1044	1	348	0.0	662
-gi|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	1e-168	575
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.40	111	4	0	1	333	11	121	2e-62	224
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.31	65	5	0	3174	3368	248	312	5e-34	129
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.43	56	2	0	2855	3022	177	232	2e-31	120
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	93.22	59	4	0	1404	1580	119	177	1e-30	118
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.00	25	2	0	4222	4296	312	336	6e-12	56.2
-gi|283855822|gb|GQ290312.1|	sp|P08100|OPSD_HUMAN	95.09	326	16	0	1	978	11	336	2e-180	613
-gi|18148870|dbj|AB062417.1|	sp|P08100|OPSD_HUMAN	93.39	348	23	0	1	1044	1	348	0.0	641
-gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	6e-164	559
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-gi|57163782|ref|NM_001009242.1|	sp|P08100|OPSD_HUMAN	96.55	348	12	0	1	1044	1	348	0.0	662	sp|P08100|OPSD_HUMAN	1707	336	343	0	98.56	1	0	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	1047	348
-gi|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	1e-168	575	sp|P08100|OPSD_HUMAN	1481	283	315	0	94.88	3	0	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE	1574	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.40	111	4	0	1	333	11	121	2e-62	224	sp|P08100|OPSD_HUMAN	570	107	109	0	98.20	1	0	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.31	65	5	0	3174	3368	248	312	5e-34	129	sp|P08100|OPSD_HUMAN	324	60	64	0	98.46	3	0	KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ	KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.43	56	2	0	2855	3022	177	232	2e-31	120	sp|P08100|OPSD_HUMAN	302	54	56	0	100.00	2	0	RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE	RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	93.22	59	4	0	1404	1580	119	177	1e-30	118	sp|P08100|OPSD_HUMAN	295	55	56	0	94.92	3	0	LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR	LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.00	25	2	0	4222	4296	312	336	6e-12	56.2	sp|P08100|OPSD_HUMAN	134	23	24	0	96.00	1	0	QFRNCMLTTLCCGKNPLGDDEASTT	QFRNCMLTTICCGKNPLGDDEASAT	4301	348
-gi|283855822|gb|GQ290312.1|	sp|P08100|OPSD_HUMAN	95.09	326	16	0	1	978	11	336	2e-180	613	sp|P08100|OPSD_HUMAN	1582	310	322	0	98.77	1	0	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT	983	348
-gi|18148870|dbj|AB062417.1|	sp|P08100|OPSD_HUMAN	93.39	348	23	0	1	1044	1	348	0.0	641	sp|P08100|OPSD_HUMAN	1654	325	337	0	96.84	1	0	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	1047	348
-gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	6e-164	559	sp|P08100|OPSD_HUMAN	1440	272	307	0	92.47	2	0	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE	1344	348
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_rhodopsin_vs_four_human_ext.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-gi|57163782|ref|NM_001009242.1|	sp|P08100|OPSD_HUMAN	96.55	348	12	0	1	1044	1	348	0.0	 662	sp|P08100|OPSD_HUMAN	1707	336	343	0	98.56	1	0	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	1047	348
-gi|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	1e-168	 575	sp|P08100|OPSD_HUMAN	1481	283	315	0	94.88	3	0	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE	1574	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.40	111	4	0	1	333	11	121	2e-62	 224	sp|P08100|OPSD_HUMAN	570	107	109	0	98.20	1	0	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.31	65	5	0	3174	3368	248	312	5e-34	 129	sp|P08100|OPSD_HUMAN	324	60	64	0	98.46	3	0	KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ	KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.43	56	2	0	2855	3022	177	232	2e-31	 120	sp|P08100|OPSD_HUMAN	302	54	56	0	100.00	2	0	RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE	RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	93.22	59	4	0	1404	1580	119	177	1e-30	 118	sp|P08100|OPSD_HUMAN	295	55	56	0	94.92	3	0	LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR	LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR	4301	348
-gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.00	25	2	0	4222	4296	312	336	6e-12	56.2	sp|P08100|OPSD_HUMAN	134	23	24	0	96.00	1	0	QFRNCMLTTLCCGKNPLGDDEASTT	QFRNCMLTTICCGKNPLGDDEASAT	4301	348
-gi|283855822|gb|GQ290312.1|	sp|P08100|OPSD_HUMAN	95.09	326	16	0	1	978	11	336	2e-180	 613	sp|P08100|OPSD_HUMAN	1582	310	322	0	98.77	1	0	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT	983	348
-gi|18148870|dbj|AB062417.1|	sp|P08100|OPSD_HUMAN	93.39	348	23	0	1	1044	1	348	0.0	 641	sp|P08100|OPSD_HUMAN	1654	325	337	0	96.84	1	0	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	1047	348
-gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	6e-164	 559	sp|P08100|OPSD_HUMAN	1440	272	307	0	92.47	2	0	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE	1344	348
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_sample.xml
--- a/test-data/blastx_sample.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,758 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>blastx</BlastOutput_program>
-  <BlastOutput_version>BLASTX 2.2.24+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db>/share/BlastDB/nr</BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>phage_suis</BlastOutput_query-def>
-  <BlastOutput_query-len>1890</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM62</Parameters_matrix>
-      <Parameters_expect>0.001</Parameters_expect>
-      <Parameters_gap-open>11</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>L;</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>phage_suis</Iteration_query-def>
-      <Iteration_query-len>1890</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|119953746|ref|YP_950551.1|</Hit_id>
-          <Hit_def>tail tape measure protein [Streptococcus phage SMP] &gt;gi|118430558|gb|ABK91882.1| tail tape measure protein [Streptococcus phage SMP]</Hit_def>
-          <Hit_accession>YP_950551</Hit_accession>
-          <Hit_len>659</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>988.407949172964</Hsp_bit-score>
-              <Hsp_score>2554</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>336</Hsp_query-from>
-              <Hsp_query-to>1889</Hsp_query-to>
-              <Hsp_hit-from>25</Hsp_hit-from>
-              <Hsp_hit-to>542</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>518</Hsp_identity>
-              <Hsp_positive>518</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>518</Hsp_align-len>
-              <Hsp_qseq>NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
-              <Hsp_hseq>NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_hseq>
-              <Hsp_midline>NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>2</Hit_num>
-          <Hit_id>gi|289551554|ref|YP_003472458.1|</Hit_id>
-          <Hit_def>Phage tail length tape-measure protein [Staphylococcus lugdunensis HKU09-01] &gt;gi|289181085|gb|ADC88330.1| Phage tail length tape-measure protein [Staphylococcus lugdunensis HKU09-01]</Hit_def>
-          <Hit_accession>YP_003472458</Hit_accession>
-          <Hit_len>1220</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>256.91395450591</Hsp_bit-score>
-              <Hsp_score>655</Hsp_score>
-              <Hsp_evalue>5.97108392092708e-66</Hsp_evalue>
-              <Hsp_query-from>342</Hsp_query-from>
-              <Hsp_query-to>1889</Hsp_query-to>
-              <Hsp_hit-from>657</Hsp_hit-from>
-              <Hsp_hit-to>1106</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>170</Hsp_identity>
-              <Hsp_positive>254</Hsp_positive>
-              <Hsp_gaps>66</Hsp_gaps>
-              <Hsp_align-len>516</Hsp_align-len>
-              <Hsp_qseq>FHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
-              <Hsp_hseq>FTLLFGKASLVRTVFGLLVGVFTSLSAPVLAVIAVIGSLVAIFVYLWKTNDGFREACINAWNVIKTTVSTVVTVIVAFVKSIWGGLVAWWQQNHVLIQAAATVVWNAIKTVIMTVMNALGPSMKTAWEVIKQAVIIVWEFIKTYVQVAIAVVSGVIKTVMQLITGDWSGAWNTIKQTAMTVWNLIKS-------GATAIFNA----LKVALSAIWNAIKSAASGAWNDMKAVIVAAVNYIKNRVQAQWNTLKAITTGVWNGIKAVISAVWNAIKSFVTSSVSKVKSSVSSGFNSVRNV-------VRSVMSA---------------VKSFISSAWNGVKSIVSGAVGAVKSFVSSGFNAVRNTVSSIMSRVKGIISSI-----------WNSIKSTVSNAVHNMTSA----------------------MSSGMSRMGSAVHSGMSRVSSAVRNGISGAYNAVRGGVYRMVSAGADLARGIARGIMNMAGYVMSRARALASRAVSAIKSALRIHS</Hsp_hseq>
-              <Hsp_midline>F LL    S +  +F  LVG+   +SAP+ AVI VI +LVA FV L+ TN+ FR     AW  IK+ +ST V  +V+FV  +WG +VAWW +N  LI+  A  VWNAI+TV+ TVM AL P ++TAW++I   V  V   IKT V   + VV G+IK VMQ+I GDWSGAW T+K  A T+W  IKS       G   IF      LK     +W  I +     W+ +K  +  A+  +   +Q    +++     VWN I  V S +W AI + V S ++ +   + +    ++ V       +++V +A               +K  IS+AW  +K+  S    A+ +F+S  +  ++   S+    +K  IS++           WN+IK+++SNA++N+ SA                      +S+G + + S V +   R+ SAVR G   A NA R  +   +S G DL  G   G+   AG ++       S A+   K  L I S</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>3</Hit_num>
-          <Hit_id>gi|223044325|ref|ZP_03614360.1|</Hit_id>
-          <Hit_def>phage tape measure protein [Staphylococcus capitis SK14] &gt;gi|222442293|gb|EEE48403.1| phage tape measure protein [Staphylococcus capitis SK14]</Hit_def>
-          <Hit_accession>ZP_03614360</Hit_accession>
-          <Hit_len>1320</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>252.67675917082</Hsp_bit-score>
-              <Hsp_score>644</Hsp_score>
-              <Hsp_evalue>1.12609769207128e-64</Hsp_evalue>
-              <Hsp_query-from>393</Hsp_query-from>
-              <Hsp_query-to>1889</Hsp_query-to>
-              <Hsp_hit-from>655</Hsp_hit-from>
-              <Hsp_hit-to>1193</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>165</Hsp_identity>
-              <Hsp_positive>275</Hsp_positive>
-              <Hsp_gaps>54</Hsp_gaps>
-              <Hsp_align-len>546</Hsp_align-len>
-              <Hsp_qseq>LVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTA---ETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLV---------------QVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVG-------PIWDWIKTT-------VSNAITAVWEIIQNIMTSIQTTW----DTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVS-----------AVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
-              <Hsp_hseq>LGGVLAALSGPVGIVIAAVAAVIAIFVALWNSSETLRNALTDAWNAIASSVGAAIQAVLGFLGDLFGRA-------QEILAPLAPMFQQVWSQIVAIVDTAVNVIAPMVKQAFNTVVAVVKVAWEIIKAVIKISMEVILSTIVALLQLLTGDWRGAWQTMSKAGAEIWKAIVEMAKNIWSILGDYLKQSWQNIVDGFSAIFGPLAGIAGSIWNGIVNIVKTVVSGLGAFLTSIWTAIVTSAQVQWSIIATVAQTIWSAIVNVIVTVVTTLVSILATIWTTIVTVASTIWTTLVTVSQTIWTIIVTTITTIVTTLGTILSAIWTGIVTVATTIWTTLVTVAQTIWTLIVTTITTIISTLVTIITTVWTTIVSVTSTIWSSLVAIAQTIWSSVLSIISGIVGVIVAIVTGNWSLLRSSTASIMSGIAGLISAVWNSITSVISSAVSNAVSTAVSGFFNMLSSIGSAMHGIVSSVLSGMMSVVNSVRSGVSNALSAVRNFIGHFTQAGTDLIMGMVNGIKNAAINVVNAAKGVASSAINAVRSVLNSHS</Hsp_hseq>
-              <Hsp_midline>L G++A +S P+  VI  +AA++A FV L+N++E  R  +  AW AI S++  A++AV+ F+ DL+G+        QE++   A   + VW+ I  +V+T +  + P+V+ A++ ++AVV     +IK V+   ++V+L  I A++Q++ GDW GAW+T+      IW+ I  +                Q  +DG   IF        SIW+ +   +  VV         IW  I T+       ++     +W  I N++ ++ TT      T+W  I TVAS IWT + T   ++ T I   I T +  + T+ SA W  I  V   I  T+V +    + LI   I+     + T  + +W  I +  S IW  +   A T W  + + IS ++  I + +   W+ +++S ++ ++ I       WN+I S IS+A+ N  ST  +G+ N++S++ +A   IVS           +VR+G  NA++A RNFI +    G DLI G V G+K AA  +++A  G  S AI+  + +L   S</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>130.568493605019</Hsp_bit-score>
-              <Hsp_score>327</Hsp_score>
-              <Hsp_evalue>6.45396672852224e-28</Hsp_evalue>
-              <Hsp_query-from>384</Hsp_query-from>
-              <Hsp_query-to>1796</Hsp_query-to>
-              <Hsp_hit-from>844</Hsp_hit-from>
-              <Hsp_hit-to>1309</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>101</Hsp_identity>
-              <Hsp_positive>215</Hsp_positive>
-              <Hsp_gaps>79</Hsp_gaps>
-              <Hsp_align-len>508</Hsp_align-len>
-              <Hsp_qseq>FAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVM----QMINGDWSG-------AWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMS-VLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKS--------------------NIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI--STAIENIKSTVSNG---WNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEG</Hsp_qseq>
-              <Hsp_hseq>FSAIFGPLAGIAGSI-------------------------------WNGIVNIVKTVVSGLGAFLTSIWTAIVTSAQVQWSIIATVAQTIWSAIVNVIVTVVTTLVSILATIWTTIVTVASTIWTTLVTVSQTIWTIIVTTITTIVTTLGTILSAIWTGIVTVATTIWTTLVTVAQTIWTLIVTTITTIISTLVTIITTVWTTIVSVTSTIWSSLVAIAQTIWSSVLSIISGIVGVIVAIVTGNWSLLRSSTASIMSGIAGLISAVWNSITSVISSAVSNAVSTAVSGFFNMLSSIGSAMHGIVSSVLSGMMSVV--------NSVRSGVSNALSAVRNFIGHFTQAGTDLIMGMVNGIKNAAINVVNAAKGVASSAINAVRSVLNSHSPSRVMMGIGGDFGEGFKIGIDDKKKSVANIAGGLGSSAVKA---VKNAVNPTDVLSDVRSTLKNSNLKIPNIQGDIKNASASANANITHTHEYKTNPSQRVVTVQMDVNNDALTHIVNG</Hsp_hseq>
-              <Hsp_midline>F+ + G +AGI+  I                               W  I + + T V  + +F+  +W  +V        +I   A+T+W+AI  V+ TV+T L+ I+ T W  I+ V +T+   + TV  T   +++  I  ++     +++  W+G        W TL  VA TIW  I + +   I  LV I  T    + S+  T+W +++A+   IW  + + +S  +  +  I+    + ++++  ++ + I+ + S +W +I++ + S V   +   +  +  ++ ++ SA   I+ +V + ++  +        + ++  +SNA   ++        A T  + G+  GIK AA       K   S+ +  ++S                      +   ++ K S++N    + S+A  A   +K+A+  +  + +++ST+ N      N+   + NA     + +    +   N ++  ++  + V  D +   V G</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>4</Hit_num>
-          <Hit_id>gi|268611153|ref|ZP_06144880.1|</Hit_id>
-          <Hit_def>hypothetical protein RflaF_16865 [Ruminococcus flavefaciens FD-1]</Hit_def>
-          <Hit_accession>ZP_06144880</Hit_accession>
-          <Hit_len>1158</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>239.194774013712</Hsp_bit-score>
-              <Hsp_score>609</Hsp_score>
-              <Hsp_evalue>1.28842161409548e-60</Hsp_evalue>
-              <Hsp_query-from>78</Hsp_query-from>
-              <Hsp_query-to>1847</Hsp_query-to>
-              <Hsp_hit-from>440</Hsp_hit-from>
-              <Hsp_hit-to>1042</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>183</Hsp_identity>
-              <Hsp_positive>291</Hsp_positive>
-              <Hsp_gaps>85</Hsp_gaps>
-              <Hsp_align-len>639</Hsp_align-len>
-              <Hsp_qseq>NLVAGLGQKDADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVW-----------NAISTVASNIWTAISTTVMSVLTTIWGYIQT---------------YLELIKTVWSA------------------AWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS</Hsp_qseq>
-              <Hsp_hseq>NLGGQLTILKSQLQELAISFGEILMPAIRAIVSKIQGFIDKLNAMDPATKETIVKIALVAAALGPLLVVVGKTMVGVGKLMQLVANLPT-------IIAGAKAAFTSFGAAIG---GISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWNQIKSIFDNFCQGIVDRVNAL--------GFDFKNISEVIKAVWDGL-------CKFLAPVFE-------GVFQQVANIFKAVTD----IILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVWTSIKNFFVNIWNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVKGVAN</Hsp_hseq>
-              <Hsp_midline>NL   L    + ++ L  + GE +   +R + + +    D L  + P  K     + L+A A GP L+++G     +  ++ + + +         + +G  A    F   +G   GISAP+ AVI V+AALVA FV L+ TNE+FR K+ A W  IKS      + +V  V  L          + + I +  + VW+ +          L P+ +        V   V N+ K V D    ++L I+   + +  GDWS  W+ +KG+   +W  +K  ++  ++ L  +F T L  +K  W  VW +I      IW+ IK  ++  + A+      I T I+  +  +W           N I TV + +W AI T +  VL  IW  I T               +  L +T++ A                  AWE IKAV   +L  I  ++   ++ I  AI+   + I    S +WNAI++F+SG+   I +  S+ W  IK  I+N +  I + +   WN I   IS  LN I S   + WN IK+ ++  +  IK+TVSN W+++ + VT     I   +  GF+ AVN  +N  S A   G D+ING V G+K   G++ DAV G  +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>141.354081730704</Hsp_bit-score>
-              <Hsp_score>355</Hsp_score>
-              <Hsp_evalue>3.65629455324605e-31</Hsp_evalue>
-              <Hsp_query-from>543</Hsp_query-from>
-              <Hsp_query-to>1856</Hsp_query-to>
-              <Hsp_hit-from>547</Hsp_hit-from>
-              <Hsp_hit-to>938</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>103</Hsp_identity>
-              <Hsp_positive>183</Hsp_positive>
-              <Hsp_gaps>52</Hsp_gaps>
-              <Hsp_align-len>441</Hsp_align-len>
-              <Hsp_qseq>ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNL---VSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAI</Hsp_qseq>
-              <Hsp_hseq>ISAPVVAVIAVVAALVAAFVHLWRTNEDF-RNKITAIWNQIKSIFDNFCQGIVDRVNA-------------------LGFDFKNISEVIKAV-------WDGLCKFLAPVFEGVFQQVANIFKAVTDIILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVWTSIKNFFVNIWNGIKNFITGVVNAI-----------KNFFTTIWTGIKNFF-------VGIWTAIYNSVAEKIN----LIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFI</Hsp_hseq>
-              <Hsp_midline>IS  V AV++ V  L    V  W  N++  R     +WN I+++ +     ++  V                     +    K +  +IKAV       W G  + L  V   +++ + ++ +   D ++ I    +      W  VW  I  +   +W+++K T+ N +  +  +    +  ++  W  VW +I     NIW  I   +  V+  I           K  ++  W  IK  F       VG+ T  ++ + + I+    +IKT  + +WNAI T +S +   I    ST W+ I   IS ++   +   ET +  I   IS  ++ I      AW NIK+ ++  +E IKS +   WN +   ++TV +A   ++S V     + ++   N I + IS   + I   +     A   ++ AV  A+SG I</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>140.198483002952</Hsp_bit-score>
-              <Hsp_score>352</Hsp_score>
-              <Hsp_evalue>8.14537447802119e-31</Hsp_evalue>
-              <Hsp_query-from>522</Hsp_query-from>
-              <Hsp_query-to>1844</Hsp_query-to>
-              <Hsp_hit-from>722</Hsp_hit-from>
-              <Hsp_hit-to>1121</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>116</Hsp_identity>
-              <Hsp_positive>190</Hsp_positive>
-              <Hsp_gaps>77</Hsp_gaps>
-              <Hsp_align-len>459</Hsp_align-len>
-              <Hsp_qseq>WEAIKSAISTAVEAVVSFVMDLW--------GQMVAWWN---ENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN--GWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLI-----NGFVEGVKGAAGRLIDAVGGAV</Hsp_qseq>
-              <Hsp_hseq>WNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAI----HTAIT-------TVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAIS-----------GFISGVLNTISSVVSSIWNGIKNTVTNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNF-------IKNLASQAFQWGADII---------------NGIVNGIKNCIGKVADAVKGVANKIKSFLHFSVPD-EGTLADFESW--------------MPDFMQGLAQGINKSKKYVEKAISGVADAMTIAMNSDFNVDMSGVTGAMVGAGGTTV</Hsp_hseq>
-              <Hsp_midline>W  IK+ I+  V A+ +F   +W        G   A +N   E   LI+     VWNAI T +  V+ A+  ++ T W  I   ++ +L   + + +T  + +  II  VM  I+   + AWE +K V   + E IKS+++   + +     T +        TV   I  V+  +W+ I + +S  + A+W +I +I  SI+       NAI  V S +W AIS           G+I   L  I +V S+ W  IK     IL TI   V+  +D +K A++     IK      +NA   F       IK  AS A++W    I               N I   I N +  +  A +   N IKS +  ++ + + T+++   W              +     G    +N ++ ++  AIS   D +     + F   + G  G ++ A G  V</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>115.160510568324</Hsp_bit-score>
-              <Hsp_score>287</Hsp_score>
-              <Hsp_evalue>2.80602663410135e-23</Hsp_evalue>
-              <Hsp_query-from>501</Hsp_query-from>
-              <Hsp_query-to>1694</Hsp_query-to>
-              <Hsp_hit-from>770</Hsp_hit-from>
-              <Hsp_hit-to>1144</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>100</Hsp_identity>
-              <Hsp_positive>176</Hsp_positive>
-              <Hsp_gaps>39</Hsp_gaps>
-              <Hsp_align-len>406</Hsp_align-len>
-              <Hsp_qseq>RTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWET----LKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENI-KSTVSNGWNNLVSTV---TNAGPRIVS</Hsp_qseq>
-              <Hsp_hseq>KTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVL--------NTISSVVSSIWNGIKNTVTNI-------LNTIKTTVSNIWDSVKNAVTQKITAI-------KDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVK----GVANKIKSFLHFSVPDEGTLAD-----FESWMPDFMQGLAQGINKSKKYVEKAISGVADAMTIAMNSDFNVDMSGVTGAMVGAGGTTVVNNYNNDNSRTVNQTNNSPKSLS</Hsp_hseq>
-              <Hsp_midline>+T +   W AI +AIS  + A+ + +  +W  +  + +   E  R   ET++ AI  ++  VM  +   + TAW+ I AVVT VL  IK+V++T    +   I  VM  I+   S  W      + GV   IW  I S+     D +        A + ++W+ + G I  V+         T+S+ ++++W  I+N +T+I        N I T  SNIW ++   V   +T I        + I   ++AA   IK + +        ++ G  + IK  I    + +K     + N I +FL        T A       ++ + + M  +   I  +   ++ +IS   + +  A  + +N   S ++ A+     +TV N +NN  S     TN  P+ +S</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>90.8929372855311</Hsp_bit-score>
-              <Hsp_score>224</Hsp_score>
-              <Hsp_evalue>5.66707902872949e-16</Hsp_evalue>
-              <Hsp_query-from>492</Hsp_query-from>
-              <Hsp_query-to>1148</Hsp_query-to>
-              <Hsp_hit-from>811</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>67</Hsp_identity>
-              <Hsp_positive>106</Hsp_positive>
-              <Hsp_gaps>29</Hsp_gaps>
-              <Hsp_align-len>241</Hsp_align-len>
-              <Hsp_qseq>EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDT-----------GLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWD-----------WIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNI</Hsp_qseq>
-              <Hsp_hseq>EAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTV-------TNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVKGVANKI</Hsp_hseq>
-              <Hsp_midline>E FR   +  +EAI   IS  ++ +   +   W  + A      E I+   ETVWNAI T + TVM A+  ++ T W+ I + ++ V+N I +V+ +            L  +  ++ AV   I+G  SG   T+  V  +IW GIK+ V         I  T    + +IWD+V   +   +  I D           +IK   S A     +II  I+  I+     V +A+  VA+ I</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>6</Hsp_num>
-              <Hsp_bit-score>51.9877801178785</Hsp_bit-score>
-              <Hsp_score>123</Hsp_score>
-              <Hsp_evalue>0.000291728300853117</Hsp_evalue>
-              <Hsp_query-from>1158</Hsp_query-from>
-              <Hsp_query-to>1883</Hsp_query-to>
-              <Hsp_hit-from>547</Hsp_hit-from>
-              <Hsp_hit-to>775</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>50</Hsp_identity>
-              <Hsp_positive>102</Hsp_positive>
-              <Hsp_gaps>35</Hsp_gaps>
-              <Hsp_align-len>253</Hsp_align-len>
-              <Hsp_qseq>ISTTVMSVLTTIWGYIQTYLELIKT------VWSAAWEIIKAVFAAILLTIVGLVTG-NFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTI----KSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGI</Hsp_qseq>
-              <Hsp_hseq>ISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWNQIKSIFDNFCQGIVDRVNALGFDF-----KNISEVIKA----VWDGLCKFLAPVFEGVFQQVANIFKAVTDIILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVW---------------TSIKNFFVNIWNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITV</Hsp_hseq>
-              <Hsp_midline>IS  V++V+  +   +  ++ L +T        +A W  IK++F      IV  V    FD       N  E+IK     +W+ +  FL+ ++EG+    +  ++ +   I N++         +    W+ IK       N +K   +N  N + +   T ++ +K    N W               ++++  F N  N  +NFI+  ++   +       G+K     +  A+  +V+  I+  K ++ +</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>5</Hit_num>
-          <Hit_id>gi|268610688|ref|ZP_06144415.1|</Hit_id>
-          <Hit_def>hypothetical protein RflaF_14482 [Ruminococcus flavefaciens FD-1]</Hit_def>
-          <Hit_accession>ZP_06144415</Hit_accession>
-          <Hit_len>1444</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>234.572379102704</Hsp_bit-score>
-              <Hsp_score>597</Hsp_score>
-              <Hsp_evalue>3.17349283264528e-59</Hsp_evalue>
-              <Hsp_query-from>78</Hsp_query-from>
-              <Hsp_query-to>1847</Hsp_query-to>
-              <Hsp_hit-from>440</Hsp_hit-from>
-              <Hsp_hit-to>1042</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>185</Hsp_identity>
-              <Hsp_positive>294</Hsp_positive>
-              <Hsp_gaps>85</Hsp_gaps>
-              <Hsp_align-len>639</Hsp_align-len>
-              <Hsp_qseq>NLVAGLGQKDADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVS-------NAITAVWEIIQN----IMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQT---------------YLELIKTVWSA------------------AWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS</Hsp_qseq>
-              <Hsp_hseq>NLGGQLTILKSQLQELAISFGEILMPAIRSIVSRIQGLIDKFNALSPATKETIVKVALVAATLGPLLVVVGKTMVGVGKLMQLVA------NLPTIIASAKAA----FTSFGAAIGGISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWEQIKSIFSGFCQGIVDRINALGFDF---------------KNITEVIKAVWDGLCKFLKPIFEGQFQ-------QIANIFKAVTD----IILSVLDIFVGIFTGDWSRVWDGIKGIFVAVWNFIKDTLKNALNMICGIFGTDLGEVKEFWVGVWTSIKNFFVNIWNGIKNFISSVLGGIKNFFTTIWTGIKNFFVGIWTAIYSSVSEKINLIKTVITVVWNAIHTAISTVLNAIWSVITTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVAN</Hsp_hseq>
-              <Hsp_midline>NL   L    + ++ L  + GE +   +R++ + +  + D    L+P  K     + L+A   GP L+++G     +  ++ + +      N   ++ S  +A    F      I GISAP+ AVI V+AALVA FV L+ TNE+FR K+ A WE IKS  S   + +V  +  L                   + +   I+ V + +   L PI +  +         + N+ K V D    ++L ++   + +  GDWS  W+ +KG+   +W  IK  ++ A++ +  IF T L  +K  W  VW +I      IW+ IK  +S       N  T +W  I+N    I T+I ++     N I TV + +W AI T + +VL  IW  I T               +  L +T++ A                   WE IKA+   +L  I  ++   ++ I  AIS   + I    S +WNAI+ F+SG+   I +  S+ W  IK  I+N +  I + +   WN I   IS  LN I S   + WN IK+ ++  +  IK+TVSN W+++ + VT     I   +  GF+ AVN  +N  S A   G D+IN  V G+K   G++ DAV G  +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>167.932852469002</Hsp_bit-score>
-              <Hsp_score>424</Hsp_score>
-              <Hsp_evalue>3.64782449590402e-39</Hsp_evalue>
-              <Hsp_query-from>501</Hsp_query-from>
-              <Hsp_query-to>1856</Hsp_query-to>
-              <Hsp_hit-from>770</Hsp_hit-from>
-              <Hsp_hit-to>1245</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>121</Hsp_identity>
-              <Hsp_positive>216</Hsp_positive>
-              <Hsp_gaps>54</Hsp_gaps>
-              <Hsp_align-len>491</Hsp_align-len>
-              <Hsp_qseq>RTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWET----LKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLT----TIWGYIQTYLELIKTVWSAAW----EIIKAVFAAI---LLTIVGLVTGNFDLIKQ------------AISNAW---------EIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGW---NNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAI</Hsp_qseq>
-              <Hsp_hseq>KTVITVVWNAIHTAISTVLNAIWSVITTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVL--------NTISSVVSSIWNGIKNTVTNI-------LNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVANKIKSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNANAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVVQAVWDAMPDTV</Hsp_hseq>
-              <Hsp_midline>+T +   W AI +AIST + A+ S +  +W  +  + +   E  R   ET++ AI  ++  VM  +   +   W+ I A+VT VL  IK+V++T    +   I  VM  I+   S  W      + GV   IW  I S+     D +        A + ++W+ + G I  V+         T+S+ ++++W  I+N +T+I        NAI T  SNIW ++   V   +T    TI       +  IK + S A+    +II  + + I   +  +   V G  + IK             A   +W         + I   TS + +A+ +F  G+ E I +    A   + T++   MT +   ++T W N   +I   ++ I S   + W  I S I TA+ENI++ ++  W   ++++S   +   +IV+ V T   N +   +  I + ++   + ++G V     A   ++ AV  A+   +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>161.769659254324</Hsp_bit-score>
-              <Hsp_score>408</Hsp_score>
-              <Hsp_evalue>2.61420693292496e-37</Hsp_evalue>
-              <Hsp_query-from>492</Hsp_query-from>
-              <Hsp_query-to>1832</Hsp_query-to>
-              <Hsp_hit-from>811</Hsp_hit-from>
-              <Hsp_hit-to>1322</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>123</Hsp_identity>
-              <Hsp_positive>220</Hsp_positive>
-              <Hsp_gaps>75</Hsp_gaps>
-              <Hsp_align-len>517</Hsp_align-len>
-              <Hsp_qseq>EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDT-----------GLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAI--------------------------DGLVQIFQTGLAFLKSIWDTV--WGT---------IMAVVGPIWDWIKTTVSNAITAV----------------W--EIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMS----VLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAV</Hsp_qseq>
-              <Hsp_hseq>EAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKG-VANKIKSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNA----NAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVVQAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAMNAVYKAVKDKVNSSWSWGRDLMQNLINGITYMLGSLINTV</Hsp_hseq>
-              <Hsp_midline>E FR   +  +EAI   IS  ++ +   +++ W  + A      E I+   ETVWNAI T + TVM A+  +V T W+ I   ++ V+N I +V+ +            L  +  ++ AV   I+G  SG   T+  V  +IW GIK+ V   +                          D +V  F   + F+K++      WG          I   +G + D +K  V+N I +                 W  + +Q +   I      V +A+++ A  +   IS+ + +    V+T++ G++    + +KTVW+ A     A   A +  I   +T  +  I   I  A E I+   +  W A+++ +S   +GIK   +  W  +K  I      IKS + T W  +   +  A+N IKS  +  W+ +   + +A+  +K  V + W+ + S + +    +  AV    +    A ++ ++++ S G DL+   + G+    G LI+ V</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>123.249701662589</Hsp_bit-score>
-              <Hsp_score>308</Hsp_score>
-              <Hsp_evalue>1.03039235764918e-25</Hsp_evalue>
-              <Hsp_query-from>510</Hsp_query-from>
-              <Hsp_query-to>1859</Hsp_query-to>
-              <Hsp_hit-from>905</Hsp_hit-from>
-              <Hsp_hit-to>1377</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>108</Hsp_identity>
-              <Hsp_positive>204</Hsp_positive>
-              <Hsp_gaps>63</Hsp_gaps>
-              <Hsp_align-len>493</Hsp_align-len>
-              <Hsp_qseq>VQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAV--------MQMINGDWSG-------AWETLKGVAGTIWEGIKSLVQVAI--DGLVQIFQTGLA-FLKSIWD-------TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVT------------GNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLIN------GFVEGVKGAAGRLIDAVGGAVSGAID</Hsp_qseq>
-              <Hsp_hseq>ISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVANKI----KSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNANAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLD-IKSVVTTTWEAVSGVVRTAVNA-----------IKSVVQAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAMNAVYKAVKDKVNSSWSWGRDLMQNLINGITYMLGSLINTVA----DVARSIWEYLHFSVPEKGALTDVEEWMPDFMKGLAKGINKSKKYVEAAVSGVAD</Hsp_hseq>
-              <Hsp_midline>+ + W +IK  I+  + A+ + V  +W  +  + +     I     ++WN I+  V  ++ A+   V   WD +   VT  +  IK  +  G    +  IK +          +IN   SG         + +KGVA  I    KS +  ++  +G +  F++ +  F++ + D        V   + +  G + + I + + NA++ V   +Q  MT +  T  TVW   +       + IS+ + S   TI   I+T LE I+ V +  W+ + +V +A L  I  +VT            G  D IK  ++  WE +        NA           IK+     W+ +  T+ + M  +K  + + W+ IK+ I + L  ++ A  NA N +  A+   + +  S   +   NL++ +T     +++ V     +   +   ++  ++   G L +       F++G+     +    V  AVSG  D</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>71.6329584896635</Hsp_bit-score>
-              <Hsp_score>174</Hsp_score>
-              <Hsp_evalue>3.55787431696712e-10</Hsp_evalue>
-              <Hsp_query-from>486</Hsp_query-from>
-              <Hsp_query-to>1343</Hsp_query-to>
-              <Hsp_hit-from>1138</Hsp_hit-from>
-              <Hsp_hit-to>1400</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>60</Hsp_identity>
-              <Hsp_positive>128</Hsp_positive>
-              <Hsp_gaps>35</Hsp_gaps>
-              <Hsp_align-len>292</Hsp_align-len>
-              <Hsp_qseq>TNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTV--MSVLTTIWGYIQTYLELIKTVWSAAWEIIKA----VFAAILLTIVGLVTGNFDLIKQAISN</Hsp_qseq>
-              <Hsp_hseq>TMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVV-----------QAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAM-------NAVYKAVKDKVNSSWSWGR-----------DLMQNLINGITYMLGSLINTVADVARSIWEYLHFSVPEKGALTDVEEWMPDFMKGLAKGINKSKKYVEAAVSGVADAMTLTMQSGLNVDMDGISGAMMN</Hsp_hseq>
-              <Hsp_midline>T  +  + + + W+ I S I TA+E + + +   W  + +  +   + I++    VW A++ +++T    +  +V T W+ +  VV T +N IK+VV           +AV   +      A   +K    +IW+GIKS +   + G+       +       + V+  +   V   W W +           +++QN++  I     ++ N ++ VA +IW  +  +V     LT +  ++  +++ +    + + + ++A    V  A+ LT+   +  + D I  A+ N</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>6</Hsp_num>
-              <Hsp_bit-score>53.9137779974652</Hsp_bit-score>
-              <Hsp_score>128</Hsp_score>
-              <Hsp_evalue>7.67706873813937e-05</Hsp_evalue>
-              <Hsp_query-from>894</Hsp_query-from>
-              <Hsp_query-to>1883</Hsp_query-to>
-              <Hsp_hit-from>467</Hsp_hit-from>
-              <Hsp_hit-to>775</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>73</Hsp_identity>
-              <Hsp_positive>133</Hsp_positive>
-              <Hsp_gaps>43</Hsp_gaps>
-              <Hsp_align-len>341</Hsp_align-len>
-              <Hsp_qseq>IKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKT------VWSAAWEIIKAVFAAILLTIVGLVTG-NFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTI----KSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGI</Hsp_qseq>
-              <Hsp_hseq>IRSIVS-RIQGLIDKFNALSPATKETIVKV-ALVAATLGPLLVVVGKTMVG-VGKLMQLVANLPTIIASA-----KAAFTSFGAAIGGISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWEQIKSIFSGFCQGIVDRINALGFDF-----KNITEVIKA----VWDGLCKFLKPIFEGQFQQIANIFKAVTDIILSVLDIFVGIFTGDWSRVWDGIKGIFVAVWNFIKDTLKNALNMICGIFGTDLGEVKEFWVGVW---------------TSIKNFFVNIWNGIKNFISSVLGGIKNFFTTIWTGIKNFFVGIWTAIYSSVSEKINLIKTVITV</Hsp_hseq>
-              <Hsp_midline>I+S+V   I GL+  F       K     V   + A +GP+   +  T+   +  + +++ N+ T I +       A  T        IS  V++V+  +   +  ++ L +T        +A WE IK++F+     IV  +    FD       N  E+IK     +W+ +  FL  I+EG     +  ++ +   I +V+         +    W+ IK       N IK   +NA N I     T +  +K      W               ++++  F N  N  +NFIS+ +    +       G+K     +  A+  +VS  I+  K ++ +</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>6</Hit_num>
-          <Hit_id>gi|153811333|ref|ZP_01964001.1|</Hit_id>
-          <Hit_def>hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] &gt;gi|149832460|gb|EDM87544.1| hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174]</Hit_def>
-          <Hit_accession>ZP_01964001</Hit_accession>
-          <Hit_len>1228</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>219.934795217844</Hsp_bit-score>
-              <Hsp_score>559</Hsp_score>
-              <Hsp_evalue>8.08889755547188e-55</Hsp_evalue>
-              <Hsp_query-from>108</Hsp_query-from>
-              <Hsp_query-to>1847</Hsp_query-to>
-              <Hsp_hit-from>493</Hsp_hit-from>
-              <Hsp_hit-to>1073</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>176</Hsp_identity>
-              <Hsp_positive>285</Hsp_positive>
-              <Hsp_gaps>81</Hsp_gaps>
-              <Hsp_align-len>621</Hsp_align-len>
-              <Hsp_qseq>ADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKT-------TVSNAITAVWE-IIQNI---MTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELI----KTVWS-------AAWEIIK-AVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIW------------EGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTS-ISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS</Hsp_qseq>
-              <Hsp_hseq>SQLQELAISFGEILMPKIRDIVTHIQNFVDKLNAMDEGQKETILRIGMFVAALAPMLMGLGKVITFSANVSRALGTLSAG-----LVKAGG--FSGVFTKALGLI---TSPAAIVVGVIAAITAVIIHLWNTNEDFRNTITAIWQKIKDAFTTFAAGI---------------SERLSALGITFSDVTSAIKTIWDGFCNLLAPVLEAAFSTIAIALQTAFNVI-----------LGIWDVFSAVFSGDWSGAWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVFLGWFGTNWETVWNGVKTFFEGIWNGISSFFEGIWNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTT----IWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATS</Hsp_hseq>
-              <Hsp_midline>+ ++ L  + GE +   +R++   +    D L  +   QK     +G+   A  P LM LG +    + V      +S       L+ +GG   S +F K +G+I   ++P   V+GVIAA+ A  + L+NTNE+FR  + A W+ IK A +T    +               +E    +  T   V +AI+T+ +     L P+++ A+  I   + T  NVI           LGI      + +GDWSGAWE +KG+  +IW+G+K      I  +  +    L +  + W+TVW  +      IW+ I +        +S   T VW  I+ N+    T++  T  T++NA+  V SN+W  I   V   +  I   ++   ELI    + +W        + WE IK AV  AI      ++T   + I   I+  W  I+T  + + NAI + +   W              I T  ST W  IKTT + V+  IKS ++TAWN +K S I+  +N IK+     WN IK+A+ T +  IK+TV   +N + +TVT     I +A++TG   A NA +  ++  I+     +   + G+K     + ++V  A S</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>195.667221935051</Hsp_bit-score>
-              <Hsp_score>496</Hsp_score>
-              <Hsp_evalue>1.63364171761813e-47</Hsp_evalue>
-              <Hsp_query-from>519</Hsp_query-from>
-              <Hsp_query-to>1760</Hsp_query-to>
-              <Hsp_hit-from>709</Hsp_hit-from>
-              <Hsp_hit-to>1099</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>127</Hsp_identity>
-              <Hsp_positive>197</Hsp_positive>
-              <Hsp_gaps>51</Hsp_gaps>
-              <Hsp_align-len>428</Hsp_align-len>
-              <Hsp_qseq>AWEAIKSAISTAVEAVVSFVMDLWGQM-------VAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWE-IIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQT-----YLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKT-SEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAIS</Hsp_qseq>
-              <Hsp_hseq>AWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVFLGWFGTNWE-------TVWNGVKTFFEGIWNGISSFFEGIWNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAV-----------KDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTT----FTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVI-----------NAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITT----PINAAKTAVGNAIS</Hsp_hseq>
-              <Hsp_midline>AWEAIK   S+  + +  +   + G +       + W+  N E       TVWN ++T  E +   +    +  W+ I    TTV N I T V      V   I  +   +           K V   +WE IK++VQVAI  +V++ +     +   +  +W      +  +W+ IK+ V  AI  V + II  +M +I  T  TVWNAI T     +T +   + S + T W +++       +  I T  S  W  IK  F  ++           + IK A+  AW  +K    + + N I T ++ +W  IKTA  T    IKTT+  V   +K+ + T WN IKT  S A N +K+A     N  KSA+++AI  IKST+S+ WN++ S  ++    I  A+ T     +NAA+  + NAIS</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>169.473650772671</Hsp_bit-score>
-              <Hsp_score>428</Hsp_score>
-              <Hsp_evalue>1.25373984602686e-39</Hsp_evalue>
-              <Hsp_query-from>498</Hsp_query-from>
-              <Hsp_query-to>1640</Hsp_query-to>
-              <Hsp_hit-from>746</Hsp_hit-from>
-              <Hsp_hit-to>1096</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>115</Hsp_identity>
-              <Hsp_positive>178</Hsp_positive>
-              <Hsp_gaps>50</Hsp_gaps>
-              <Hsp_align-len>391</Hsp_align-len>
-              <Hsp_qseq>FRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLK-SIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWD--------TVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIK-TVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN</Hsp_qseq>
-              <Hsp_hseq>FGTNWETVWNGVKTFFEGIWNGISSFFEGIWNGISTF-----------CTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAIN-----------FVKDNIITPVMNAISATITTVWNAIQTTFTTVINA-------IKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNA-----------IKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITTPINAAKTAVGN</Hsp_hseq>
-              <Hsp_midline>F T  +  W  +K+        + SF   +W  +  +             TVWN I T V    T +   + T ++ +  VV+ V   IK VV   +  ++ ++KA  ++I   +   WE  +    ++WE IKS VQ AI+           F+K +I   V   I A +  +W+ I+TT +  I A       I +++QT W+         V NAIST  S +W  I TT  +V+  I   +QT    +K +V +     IK V   +   I   V    + IK  +   +  +KT  + IWNA           IKT  STAW  +KT ++  +   KS + +A N IK++IS+  N++KSA  + WN IK AI+T I   K+ V N</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>118.242107175663</Hsp_bit-score>
-              <Hsp_score>295</Hsp_score>
-              <Hsp_evalue>3.31465838308759e-24</Hsp_evalue>
-              <Hsp_query-from>492</Hsp_query-from>
-              <Hsp_query-to>1256</Hsp_query-to>
-              <Hsp_hit-from>854</Hsp_hit-from>
-              <Hsp_hit-to>1111</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>71</Hsp_identity>
-              <Hsp_positive>119</Hsp_positive>
-              <Hsp_gaps>23</Hsp_gaps>
-              <Hsp_align-len>268</Hsp_align-len>
-              <Hsp_qseq>EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILA-VVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKG------------VAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEI</Hsp_qseq>
-              <Hsp_hseq>ENCRDTIISVWETIKSAVQTAINFVKDNII----------TPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITTPINAAKTAVGNAISAIRSKFNFSWSL</Hsp_hseq>
-              <Hsp_midline>E  R  + + WE IKSA+ TA+  V   ++                I  T  TVWNAI+T   TV+ A+   VQTAW+ +   VVT V+N I T + T    +      V+  I      AW  +K             V  T+W  IK+ VQ  ++ +    QT    +K+   T+W  I       W+ +KT V+  I A    + + +  I++T  +VWN++ +  S+ W AI   + + +      +   +  I++ ++ +W +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>116.316109296076</Hsp_bit-score>
-              <Hsp_score>290</Hsp_score>
-              <Hsp_evalue>1.25956884194974e-23</Hsp_evalue>
-              <Hsp_query-from>510</Hsp_query-from>
-              <Hsp_query-to>1385</Hsp_query-to>
-              <Hsp_hit-from>816</Hsp_hit-from>
-              <Hsp_hit-to>1110</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>83</Hsp_identity>
-              <Hsp_positive>132</Hsp_positive>
-              <Hsp_gaps>25</Hsp_gaps>
-              <Hsp_align-len>306</Hsp_align-len>
-              <Hsp_qseq>VQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVET------------VMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVL-GIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQ-IFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWN</Hsp_qseq>
-              <Hsp_hseq>VSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRA-----------ITTPINAAKTAVGNAISAIRSKFNFSWS</Hsp_hseq>
-              <Hsp_midline>V   WE IK+ +  A+  +V  V   +  +   +    E  R T  +VW  I++ V+T            VM A+   + T W+ I    TTV+N IK+ V T    +   ++  VM  I+   S  W T+K    T+   IKS VQ A + +   +    +  +K++  TVW  I   V  + + IKTTV     AV   +  I  +I+T   T WNA+ T  +    A  + V S +  I   I +    +K+  S+ W  IK             +T   +  K A+ NA   I++K +  W+</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>7</Hit_num>
-          <Hit_id>gi|262113750|emb|CAR95417.1|</Hit_id>
-          <Hit_def>hypothetical protein [Streptococcus phage phi-m46.1]</Hit_def>
-          <Hit_accession>CAR95417</Hit_accession>
-          <Hit_len>952</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>218.779196490092</Hsp_bit-score>
-              <Hsp_score>556</Hsp_score>
-              <Hsp_evalue>1.80201837527491e-54</Hsp_evalue>
-              <Hsp_query-from>384</Hsp_query-from>
-              <Hsp_query-to>1241</Hsp_query-to>
-              <Hsp_hit-from>540</Hsp_hit-from>
-              <Hsp_hit-to>818</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>110</Hsp_identity>
-              <Hsp_positive>166</Hsp_positive>
-              <Hsp_gaps>7</Hsp_gaps>
-              <Hsp_align-len>286</Hsp_align-len>
-              <Hsp_qseq>FAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
-              <Hsp_hseq>FLPIVGIIVGIVAAI-------TLLIVGLKELWTNHEGFRTAVTEIWNSIYAFLSMIIQQISSFVMSVWGTLTTWWTENQQLILNAATTVWNAITTVIQTVMTILGPLIQASWENIKLIITAAWEMIKIVVETAINVVLGIIKAVMQVITGDWTGAWETIKQVLSMAWEGIKSLISLALNFIAQYISTAWTGIKNTISNVLSAISSVISSIWTAIQSTISSVLSAIGSTVSTIWNGISNTVSNILNGISNTVSSVWNGVKNTISNAINGARDAVSNAINAIKNLFN</Hsp_hseq>
-              <Hsp_midline>F  +VGII GI A I         L+ G   L+  +E FRT V   W +I + +S  ++ + SFVM +WG +  WW ENQ+LI   A TVWNAI TV++TVMT L P++Q +W+ I  ++T    +IK VV+T + VVLGIIKAVMQ+I GDW+GAWET+K V    WEGIKSL+ +A++ + Q   T    +K+    V   I +V+  IW  I++T+S+ ++A+   +  I   I  T   + N IS   S++W  +  T+ + +      +   +  IK +++</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>171.784848228175</Hsp_bit-score>
-              <Hsp_score>434</Hsp_score>
-              <Hsp_evalue>2.526199638793e-40</Hsp_evalue>
-              <Hsp_query-from>657</Hsp_query-from>
-              <Hsp_query-to>1871</Hsp_query-to>
-              <Hsp_hit-from>460</Hsp_hit-from>
-              <Hsp_hit-to>858</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>122</Hsp_identity>
-              <Hsp_positive>198</Hsp_positive>
-              <Hsp_gaps>18</Hsp_gaps>
-              <Hsp_align-len>411</Hsp_align-len>
-              <Hsp_qseq>NAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNV---IKTVVD--TGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG</Hsp_qseq>
-              <Hsp_hseq>NALAAIGQPILEMLIPVFQSLADIVSQLATWFTNLSSPIKEVVIIFTGILAVVGMLLPVFLGLQVAAAAMGTTVVGMITAFLPIVGIIV-----GIVAAITLLIVGLKELWTNHEGFRTAVT-EIWNSIYAFLSMIIQQISSFVMSVWGTLTTWWTENQQLILNAATTVWNAITTVIQTVMTILGPLIQASWENIKLIITAAWEMIKIVVETAINVVLGIIKAVMQVITGDWTGAWETIKQVLSMAWEGIKSLISLALNFIAQYISTAWTGIKNTISNVLSAISSVISSIWTAIQSTISSVLSAIGSTVSTIWNGISNTVSNILNGISNTVSSVWNGVKNTISNA----INGARDAVSNAINAIKNLFNFQIRWPHIPLPHF--RVSGSANPLDWLKGGIPRISIDWYAKG</Hsp_hseq>
-              <Hsp_midline>NA+  + + ++  LIP+ Q+  D++  + T   N+   IK VV   TG+  V+G++  V   +    +    T+ G+       +  +V     G+V      +  LK +W    G   AV   IW+ I   +S  I  +   + ++  ++ T W      I   A+ +W AI+T + +V+T +   IQ   E IK + +AAWE+IK V    +  ++G++     +I    + AWE IK   S  W  I + +S     I    STAW  IK TISNV++ I S I + W  I+++IS+ L+ I S     WN I + +S  +  I +TVS+ WN + +T++NA    ++  R    NA+NA +N  +  I      +  F   V G+A  L    GG    +IDW AKG</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>8</Hit_num>
-          <Hit_id>gi|77411259|ref|ZP_00787609.1|</Hit_id>
-          <Hit_def>tail tape meausure protein [Streptococcus agalactiae CJB111] &gt;gi|77162685|gb|EAO73646.1| tail tape meausure protein [Streptococcus agalactiae CJB111]</Hit_def>
-          <Hit_accession>ZP_00787609</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>215.697599882754</Hsp_bit-score>
-              <Hsp_score>548</Hsp_score>
-              <Hsp_evalue>1.52550005815421e-53</Hsp_evalue>
-              <Hsp_query-from>387</Hsp_query-from>
-              <Hsp_query-to>1241</Hsp_query-to>
-              <Hsp_hit-from>628</Hsp_hit-from>
-              <Hsp_hit-to>905</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>106</Hsp_identity>
-              <Hsp_positive>170</Hsp_positive>
-              <Hsp_gaps>7</Hsp_gaps>
-              <Hsp_align-len>285</Hsp_align-len>
-              <Hsp_qseq>AKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
-              <Hsp_hseq>APIVGIILGVIAVV-------ALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNAINGAKNAVSSAINAIKNLFN</Hsp_hseq>
-              <Hsp_midline>A +VGII G+ A +       A LV G   L+  +E FRT V   W AI + +S  ++ + SFVM +WG +  WW ENQ+LI   A TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q        +K     +  +I +VV  +W+ IK+T+S+ ++++   + ++   ++ T   V + IS   S++W  + +T+ + +      + + +  IK +++</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>172.55524738001</Hsp_bit-score>
-              <Hsp_score>436</Hsp_score>
-              <Hsp_evalue>1.48099780677056e-40</Hsp_evalue>
-              <Hsp_query-from>660</Hsp_query-from>
-              <Hsp_query-to>1871</Hsp_query-to>
-              <Hsp_hit-from>548</Hsp_hit-from>
-              <Hsp_hit-to>945</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>114</Hsp_identity>
-              <Hsp_positive>199</Hsp_positive>
-              <Hsp_gaps>12</Hsp_gaps>
-              <Hsp_align-len>407</Hsp_align-len>
-              <Hsp_qseq>AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA--IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG</Hsp_qseq>
-              <Hsp_hseq>AMAEMGDAIAATLAPILEILASLLQAVATWFSGLSEPVKQ--FIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVGIILGVIAVVALLVVGIQQLWQHHEGFRTAVT-EIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNA----INGAKNAVSSAINAIKNLFNFKIKWPHIPLPHF--SVSGSANPLDWLKGGLPKISIQWYAKG</Hsp_hseq>
-              <Hsp_midline>A+  + + +   L PI++    L+ AV T    + + V      V++G + A + ++   +         +  TI   I +   +   I G++ +    +  ++ +W    G   AV   IW+ I   +S  I  +   + +I  ++ T W      I   A+ +WTAIST + +++T +  Y+Q   E IK + + AW+IIK V    +  ++G++     +I    S AWE IK   S +W AI + +S +   I    S +W  IK T++N++ +IKS +   WN+IK++IS+ L++I S   + WN +K+ IS  +  I +TVS+ WN + ST+TNA    ++  +    +A+NA +N  +  I      +  F   V G+A  L    GG    +I W AKG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>83.5741453431014</Hsp_bit-score>
-              <Hsp_score>205</Hsp_score>
-              <Hsp_evalue>9.04763716179523e-14</Hsp_evalue>
-              <Hsp_query-from>978</Hsp_query-from>
-              <Hsp_query-to>1877</Hsp_query-to>
-              <Hsp_hit-from>540</Hsp_hit-from>
-              <Hsp_hit-to>882</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>81</Hsp_identity>
-              <Hsp_positive>141</Hsp_positive>
-              <Hsp_gaps>67</Hsp_gaps>
-              <Hsp_align-len>355</Hsp_align-len>
-              <Hsp_qseq>TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVAS---------NIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGL--VTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKT-----------AASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI-----------STAIENIKSTV----------------------SNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLL</Hsp_qseq>
-              <Hsp_hseq>TAQNTAKLAMAEMGDAIAATLAPILEILASLLQAVATWFSGLSEPVKQFIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVG--------IILGVIAVVALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTN----LLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTI</Hsp_hseq>
-              <Hsp_midline>T   T    +  + D I  T++  +  +  ++Q + T      + V   I  V S          I+ A+    M++ TTI G I     ++         II  V A + L +VG+  +  + +  + A++  W  I    S I   I++F+  IW  + T           AA+T W  I T I  +MT +   ++ +W NIK  I+ A + IK   E A N +   I           S A E IK  V                      SN WN +  T+TN    +++++++   N  N+ ++ IS+ +S  G  ++    G+K     ++  +   VS   +  K  +</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>9</Hit_num>
-          <Hit_id>gi|76786754|ref|YP_329383.1|</Hit_id>
-          <Hit_def>prophage LambdaSa04, TP901 family tail tape measure protein [Streptococcus agalactiae A909] &gt;gi|76561811|gb|ABA44395.1| prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909]</Hit_def>
-          <Hit_accession>YP_329383</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>213.386402427249</Hsp_bit-score>
-              <Hsp_score>542</Hsp_score>
-              <Hsp_evalue>7.57097807573937e-53</Hsp_evalue>
-              <Hsp_query-from>387</Hsp_query-from>
-              <Hsp_query-to>1241</Hsp_query-to>
-              <Hsp_hit-from>628</Hsp_hit-from>
-              <Hsp_hit-to>905</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>105</Hsp_identity>
-              <Hsp_positive>169</Hsp_positive>
-              <Hsp_gaps>7</Hsp_gaps>
-              <Hsp_align-len>285</Hsp_align-len>
-              <Hsp_qseq>AKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
-              <Hsp_hseq>APIVGIILGVIAVV-------ALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAIKNLFN</Hsp_hseq>
-              <Hsp_midline>A +VGII G+ A +       A LV G   L+  +E FRT V   W AI + ++  ++ + SFVM +WG ++ WW ENQ+LI     TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q        +K     +  +I  VV  +W+ IK+T+S+ ++++   + +I   ++ T   V + IS+  S +W  + +T+ + +      + + +  IK +++</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>164.851255861663</Hsp_bit-score>
-              <Hsp_score>416</Hsp_score>
-              <Hsp_evalue>3.08806866621938e-38</Hsp_evalue>
-              <Hsp_query-from>660</Hsp_query-from>
-              <Hsp_query-to>1871</Hsp_query-to>
-              <Hsp_hit-from>548</Hsp_hit-from>
-              <Hsp_hit-to>945</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>111</Hsp_identity>
-              <Hsp_positive>194</Hsp_positive>
-              <Hsp_gaps>12</Hsp_gaps>
-              <Hsp_align-len>407</Hsp_align-len>
-              <Hsp_qseq>AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA--IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG</Hsp_qseq>
-              <Hsp_hseq>AMAEMGDAIAATLAPILEVIASLLQAVATWFSGLSEPVKQ--FIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVGIILGVIAVVALLVVGIQQLWQHHEGFRTAVT-EIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNA----INGAKNAVSSAINAIKNLFNFKIKWPHIPLPHF--SVSGSANPLDWLKGGLPKISIQWYAKG</Hsp_hseq>
-              <Hsp_midline>A+  + + +   L PI++    L+ AV T    + + V      V++G + A + ++   +         +  TI   I +   +   I G++ +    +  ++ +W    G   AV   IW+ I   ++  I  +   + +I  ++ T W      I    + +WTAIST + +++T +  Y+Q   E IK + + AW+IIK V    +  ++G++     +I    S AWE IK   S +W  I + +S +   I    S +W  IK T++N++ +IK  +   WN IK++IS+ L++I S   + WN +K+ IS  +  I STVS  WN + ST+TNA    ++  +    +A+NA +N  +  I      +  F   V G+A  L    GG    +I W AKG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>115.160510568324</Hsp_bit-score>
-              <Hsp_score>287</Hsp_score>
-              <Hsp_evalue>2.80602663410135e-23</Hsp_evalue>
-              <Hsp_query-from>543</Hsp_query-from>
-              <Hsp_query-to>1391</Hsp_query-to>
-              <Hsp_hit-from>637</Hsp_hit-from>
-              <Hsp_hit-to>900</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>70</Hsp_identity>
-              <Hsp_positive>130</Hsp_positive>
-              <Hsp_gaps>19</Hsp_gaps>
-              <Hsp_align-len>283</Hsp_align-len>
-              <Hsp_qseq>ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAI</Hsp_qseq>
-              <Hsp_hseq>VIAVVALLVVGIQQLW--------QHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTV-----------SSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAI</Hsp_hseq>
-              <Hsp_midline>+   V  +V  +  LW        ++ E  R     +WNAI   +  ++  +   V + W  ++   T    +I    +T    +  +I+ +M ++      +WE +K +  T W+ IK +V+ AI+ ++ I +  +  +   W   W TI  VV  +W+ IK+ +S  ++A+ + I N    I+ T   + N+I  V SN+W  I +T+ S+L++I   +           S+ W  +KA  + +L  I   V+  ++ +K  I+NA    K   S   NAI</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>82.4185466153494</Hsp_bit-score>
-              <Hsp_score>202</Hsp_score>
-              <Hsp_evalue>2.01560327678347e-13</Hsp_evalue>
-              <Hsp_query-from>978</Hsp_query-from>
-              <Hsp_query-to>1847</Hsp_query-to>
-              <Hsp_hit-from>540</Hsp_hit-from>
-              <Hsp_hit-to>850</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>74</Hsp_identity>
-              <Hsp_positive>133</Hsp_positive>
-              <Hsp_gaps>45</Hsp_gaps>
-              <Hsp_align-len>323</Hsp_align-len>
-              <Hsp_qseq>TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVAS---------NIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGL--VTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKT-----------AASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI-----------STAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS</Hsp_qseq>
-              <Hsp_hseq>TAQNTAKLAMAEMGDAIAATLAPILEVIASLLQAVATWFSGLSEPVKQFIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVG--------IILGVIAVVALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLIS----IVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVS</Hsp_hseq>
-              <Hsp_midline>T   T    +  + D I  T++  +  +  ++Q + T      + V   I  V S          I+ A+    M++ TTI G I     ++         II  V A + L +VG+  +  + +  + A++  W  I    + I   I++F+  IW  + T           A +T W  I T I  +MT +   ++ +W NIK  I+ A + IK   E A N +   I           S A E IK  VS  W  + S ++     ++SA+     N+ N  +  ++N ++    +++    G+K     ++ ++G  VS</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-        <Hit>
-          <Hit_num>10</Hit_num>
-          <Hit_id>gi|50914476|ref|YP_060448.1|</Hit_id>
-          <Hit_def>unknown phage protein [Streptococcus pyogenes MGAS10394] &gt;gi|40218580|gb|AAR83234.1| prophage pi2 protein [Streptococcus pyogenes] &gt;gi|50261625|gb|AAT72393.1| unknown [Streptococcus pyogenes] &gt;gi|50903550|gb|AAT87265.1| unknown phage protein [Streptococcus pyogenes MGAS10394]</Hit_def>
-          <Hit_accession>YP_060448</Hit_accession>
-          <Hit_len>1039</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>207.608408788489</Hsp_bit-score>
-              <Hsp_score>527</Hsp_score>
-              <Hsp_evalue>4.15433379501178e-51</Hsp_evalue>
-              <Hsp_query-from>372</Hsp_query-from>
-              <Hsp_query-to>1241</Hsp_query-to>
-              <Hsp_hit-from>623</Hsp_hit-from>
-              <Hsp_hit-to>905</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>104</Hsp_identity>
-              <Hsp_positive>166</Hsp_positive>
-              <Hsp_gaps>7</Hsp_gaps>
-              <Hsp_align-len>290</Hsp_align-len>
-              <Hsp_qseq>LSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
-              <Hsp_hseq>LVVAAAPIVGTVLGIIAVI-------TLLVVWIQELWQNNEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFVSSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNAINGAKNVVSSAINAIKNLFN</Hsp_hseq>
-              <Hsp_midline>L V  A +VG + GI A I         LV     L+  NE FRT V   W AI + IS  ++ + +F+M +WG +  WW ENQ LI+   ETVWNAI TV++TVM+ + P ++ AW  I  ++TT   +IKTVV+T + VVLGIIKA+MQ I GDWSGAWET+KGV   +W+ I+ +V   +  + Q        +K+ +  +   I  +V  IW+ IK+ +S+ I+++   + +  + IQ T  ++ + IS+  S++W  I  ++ + +      + + +  IK +++</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>155.221266463729</Hsp_bit-score>
-              <Hsp_score>391</Hsp_score>
-              <Hsp_evalue>2.44682334507151e-35</Hsp_evalue>
-              <Hsp_query-from>660</Hsp_query-from>
-              <Hsp_query-to>1871</Hsp_query-to>
-              <Hsp_hit-from>548</Hsp_hit-from>
-              <Hsp_hit-to>945</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>111</Hsp_identity>
-              <Hsp_positive>192</Hsp_positive>
-              <Hsp_gaps>20</Hsp_gaps>
-              <Hsp_align-len>411</Hsp_align-len>
-              <Hsp_qseq>AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA------IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG</Hsp_qseq>
-              <Hsp_hseq>AMAEVGGVLAEALAPVLELLAQLLQAVANWFSN-LPGPIQTFIVIMGGLITVVGLLLPGLLA-----LQAAAVAMGTTIGGLVVAAAPIVGTVLGIIAVITLLVVWIQELWQNNEGFRTAVI-EIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFVSSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNA----INGAKNVVSSAINAIKNLFNFKISWPHIPLPHF--SVSGSANPLDWLKGGLPKISIAWYAKG</Hsp_hseq>
-              <Hsp_midline>A+  V   +  AL P+++    L+ AV     N +   + T + ++ G+I  V  ++ G  +     L+  A  +   I  LV  A      + G++ +    + +++ +W    G   AV+  IW+ I   +S  I  +   I  I  ++ T W      I      +W AIST + +V++ I  Y++     I+ + + AWEIIK V    +  ++G++      I    S AWE IK     +W AI   ++ I   I    S  W  IK T SN+++ I   + + WN IK+ IS+ +++I S   + W+ I+  IS+ +  I STVS+ WN + ++++NA    ++  +    +A+NA +N  +  IS     +  F   V G+A  L    GG    +I W AKG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>121.708903358919</Hsp_bit-score>
-              <Hsp_score>304</Hsp_score>
-              <Hsp_evalue>2.99798279087674e-25</Hsp_evalue>
-              <Hsp_query-from>543</Hsp_query-from>
-              <Hsp_query-to>1673</Hsp_query-to>
-              <Hsp_hit-from>637</Hsp_hit-from>
-              <Hsp_hit-to>1004</Hsp_hit-to>
-              <Hsp_query-frame>3</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>89</Hsp_identity>
-              <Hsp_positive>168</Hsp_positive>
-              <Hsp_gaps>29</Hsp_gaps>
-              <Hsp_align-len>387</Hsp_align-len>
-              <Hsp_qseq>ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSG--IWEGIK------TAASTAWEWIKTTISNVMTT--IKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTN</Hsp_qseq>
-              <Hsp_hseq>IIAVITLLVVWIQELW--------QNNEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFV-----------SSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNAINGAKNVVSSAINAIKNLFNFKISWPHIPLPHFSVSGSANPLDWLKGGLPKISIAWYAKGGILTKPTAFGMNEKQLMVGGEAGKEAVLPLTKQNLAAIGEGIASTMGTGGNFINVSITD</Hsp_hseq>
-              <Hsp_midline>I   +  +V ++ +LW        +N E  R     +WNAI   +  ++  +   + T W  +    T    +I+  V+T    +  +I+ VM +I      AW  ++ +  T WE IK++V+ AI  ++ I +  +  +   W   W TI  V+  +W  I+  V+  ++A+ + I N    I+ T+  + +AIS + S+IW  I + + SV+++I  ++           S+ W  I+   ++IL  I   V+  ++ IK +ISNA    K   S   NAI    +    W  I       + ++   +W+K  +  +      K  I T       +    +   ++  E      K  ++   E I ST+  G N +  ++T+</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>12310662</Statistics_db-num>
-          <Statistics_db-len>-87459526</Statistics_db-len>
-          <Statistics_hsp-len>0</Statistics_hsp-len>
-          <Statistics_eff-space>1174893963300</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/blastx_sample_converted.tabular
--- a/test-data/blastx_sample_converted.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-phage_suis	gi|119953746|ref|YP_950551.1|	100.00	518	0	0	336	1889	25	542	0.0	988
-phage_suis	gi|289551554|ref|YP_003472458.1|	32.95	516	280	6	342	1889	657	1106	6e-66	256
-phage_suis	gi|223044325|ref|ZP_03614360.1|	30.22	546	327	7	393	1889	655	1193	1e-64	252
-phage_suis	gi|223044325|ref|ZP_03614360.1|	19.88	508	328	9	384	1796	844	1309	6e-28	130
-phage_suis	gi|268611153|ref|ZP_06144880.1|	28.64	639	371	11	78	1847	440	1042	1e-60	239
-phage_suis	gi|268611153|ref|ZP_06144880.1|	23.36	441	286	7	543	1856	547	938	4e-31	141
-phage_suis	gi|268611153|ref|ZP_06144880.1|	25.27	459	266	11	522	1844	722	1121	8e-31	140
-phage_suis	gi|268611153|ref|ZP_06144880.1|	24.63	406	267	8	501	1694	770	1144	3e-23	115
-phage_suis	gi|268611153|ref|ZP_06144880.1|	27.80	241	145	3	492	1148	811	1044	6e-16	90.9
-phage_suis	gi|268611153|ref|ZP_06144880.1|	19.76	253	168	6	1158	1883	547	775	3e-04	52.0
-phage_suis	gi|268610688|ref|ZP_06144415.1|	28.95	639	369	11	78	1847	440	1042	3e-59	234
-phage_suis	gi|268610688|ref|ZP_06144415.1|	24.64	491	316	9	501	1856	770	1245	4e-39	167
-phage_suis	gi|268610688|ref|ZP_06144415.1|	23.79	517	319	9	492	1832	811	1322	3e-37	161
-phage_suis	gi|268610688|ref|ZP_06144415.1|	21.91	493	322	11	510	1859	905	1377	1e-25	123
-phage_suis	gi|268610688|ref|ZP_06144415.1|	20.55	292	197	5	486	1343	1138	1400	4e-10	71.6
-phage_suis	gi|268610688|ref|ZP_06144415.1|	21.41	341	225	10	894	1883	467	775	8e-05	53.9
-phage_suis	gi|153811333|ref|ZP_01964001.1|	28.34	621	364	16	108	1847	493	1073	8e-55	219
-phage_suis	gi|153811333|ref|ZP_01964001.1|	29.67	428	250	9	519	1760	709	1099	2e-47	195
-phage_suis	gi|153811333|ref|ZP_01964001.1|	29.41	391	226	7	498	1640	746	1096	1e-39	169
-phage_suis	gi|153811333|ref|ZP_01964001.1|	26.49	268	174	3	492	1256	854	1111	3e-24	118
-phage_suis	gi|153811333|ref|ZP_01964001.1|	27.12	306	198	4	510	1385	816	1110	1e-23	116
-phage_suis	gi|262113750|emb|CAR95417.1|	38.46	286	169	1	384	1241	540	818	2e-54	218
-phage_suis	gi|262113750|emb|CAR95417.1|	29.68	411	271	7	657	1871	460	858	3e-40	171
-phage_suis	gi|77411259|ref|ZP_00787609.1|	37.19	285	172	1	387	1241	628	905	2e-53	215
-phage_suis	gi|77411259|ref|ZP_00787609.1|	28.01	407	281	6	660	1871	548	945	1e-40	172
-phage_suis	gi|77411259|ref|ZP_00787609.1|	22.82	355	207	7	978	1877	540	882	9e-14	83.6
-phage_suis	gi|76786754|ref|YP_329383.1|	36.84	285	173	1	387	1241	628	905	8e-53	213
-phage_suis	gi|76786754|ref|YP_329383.1|	27.27	407	284	6	660	1871	548	945	3e-38	164
-phage_suis	gi|76786754|ref|YP_329383.1|	24.73	283	194	2	543	1391	637	900	3e-23	115
-phage_suis	gi|76786754|ref|YP_329383.1|	22.91	323	204	6	978	1847	540	850	2e-13	82.4
-phage_suis	gi|50914476|ref|YP_060448.1|	35.86	290	179	1	372	1241	623	905	4e-51	207
-phage_suis	gi|50914476|ref|YP_060448.1|	27.01	411	280	7	660	1871	548	945	2e-35	155
-phage_suis	gi|50914476|ref|YP_060448.1|	23.00	387	269	5	543	1673	637	1004	3e-25	121
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/four_human_proteins.fasta
--- a/test-data/four_human_proteins.fasta	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
->sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1
-MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF
-SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK
-REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER
-VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK
-CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD
-CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF
-HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL
->sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2
-MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG
-GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS
-DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD
-LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG
-KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP
-DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT
-IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE
-ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ
-QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY
-QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV
-ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD
-KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD
-QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE
-NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA
-QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK
-APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD
-EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR
-HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS
-WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ
-SQQSQPVELDPFGAAPFPSKQ
->sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4
-MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL
-QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL
-VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE
-ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL
-GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG
-CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC
-TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL
-EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE
-RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ
-NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS
-DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE
-RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL
-KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF
-PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV
-SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV
-SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG
-PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR
-EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG
-FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA
-AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV
-RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN
-CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME
-FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN
-PS
->sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
-VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
-GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
-EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
-ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
-YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/rhodopsin_nucs.fasta
--- a/test-data/rhodopsin_nucs.fasta	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
->gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
-ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCT
-TCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCT
-CATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACG
-CCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCA
-CCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGC
-CACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGT
-AAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGG
-CACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG
-CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTC
-CACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGG
-CAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCAT
-GGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGG
-TCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTG
-TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCC
-ACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA
-
->gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds
-TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTA
-CATACCCATGTCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAG
-CCATGGCAATATTCCATTCTGTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCA
-TGACCTTGTACGTCACCATCCAGCACAAGAAGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGC
-CTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTGACAATGTACTCCTCAATGAACGGATACTTC
-ATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGGTGGTGAAATCGCCCTTTGGT
-CCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCCGATTTAGTGA
-GAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT
-GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCG
-AGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTT
-CTTCTGCTATGGCCGCCTGGTGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACC
-CAGAAGGCCGAGAAAGAGGTGACCAGGATGGTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCC
-CCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGGCTCTGAGTTCGGCCCCATCTTCATGACCGT
-CCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACATCATGCTCAACAAGCAGTTC
-CGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCCTCCTCTGCCG
-CCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG
-CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGC
-GAAGTTCCCCTTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGC
-CCCCCCGAACCCCTTCGCTGCTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCA
-GCGAAGGGGTTGTCATCCGGACGCGCCAAGAATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCT
-GCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCGCACTCCGGCCGGTTCATACCTCTTATTTTT
-TTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTCAGGTCTGGTAGTGGCGGAGA
-TTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG
-
->gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds
-GTGCCCTTCTCCAACAAGACAGGCGTGGTGCGCAGTCCCTTCGAGCATCCACAGTACTACCTGGCCGAGC
-CATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTCGGCTTCCCCATCAACTTCCT
-CACGCTCTATGTCACGGTTCAGCACAAGAAGCTGCGTACGCCTCTCAACTACATCCTGCTCAACCTGGCC
-GTGGCCGACCTCTTCATGGTCTTCGGAGGCTTCACCACCACCCTCTACACCTCCCTGCATGGATACTTTG
-TCTTCGGGCCTACGGGATGCAATCTGGAGGGCTTTTTTGCCACCCTGGGAGGTATGAGCTGAGATGCGGG
-TAAGGAGGAGGCATAGAGGCATCTGGGAACAGTCCCAAGCTTGGGGTGAAGGCTAAGAGGCCTTCTTCCT
-TGTTCTGTCATTGGCGTCGTCCGAAGCCCTCACTTAATCAACAAACAGTTTGGTGGTGAGGCGCTGAGCT
-CCATTTGGAGAGGGCAGGTATCGAGCACTGTTTTATCCCCCCTGGAGTGGTGCCATTGCCTTGCTTTACA
-GCAAAGAAACTGAGGATGAGAGGAGTCGAGGGTCTTGCCAGGTCACATCATGGCAGAGACAGAGCTGAGT
-TTCAACCCTGCATCTATGTGCAGTTTCCCTTGGAGCAGCTATGTTAGGTCAGACCCACGGTGGGCACTGG
-GGAGAGAGCTGCACAAGACAGGTCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCCTGATTGCCA
-GGAGTGATGTGCAGCGCAAATGTCTGAATTCCATTATTATGTGCTCCTTCTTCCTCTGAGCCAAACATCC
-ATCTTCATGGCTCCTAGAATTGGGTCCCACCCACATGAGCAGGTCATTTTGTTTCCCTAGAGGGGAGAGG
-TCACTGCTGTGGAGGGAGGGAAGGTTCGTCCCGCTCCATGTTTCTGTTGTCTCTGCAATGCCTTTCTCTA
-GGGACTCTGCCTATTGCCCCAAGAAGGACACATTCTTCTGTAAAAACTCCCTCCTGGGTTCCCAGTCTAA
-TCAAGACCTCTAAACTGATTTCCATGTCCCTCATGAACCCAAAGCTCTAACTGAATTAAACTTCTCAGGA
-CTTACTCCACTCTCCTCGTCCATCATGCAGCCCCTCTGCCCAGCACCCTATCTCCTCTTCTTCCCAGTGT
-CTGAGCCCACTGTACCCTGAGACTTCGCTCCAGGCCTGCCCCAGGCTGCCTTCTCAGGTGCCCTCTCCCA
-CATAGGAGGAGCACGGCCTCCTTAGACAGACGTGGGGTGCAGGTTGGTGGCATGCTGACTGATAGCTGAC
-TGCCTTGCAGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTATGCA
-AGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCCTTGCCCTCACCTGGGTCATGGC
-ACTGGCCTGCGCCGCGCCCCCGCTAGTCGGCTGGTCCAGGTAATGGCACTGAACAGAAGGGAAGTGCCTC
-TGAGGTCTTCTTAGGGTCCCCCAGCTGGGACTCAAACCTAGGGCTGTCTGGTTCCAGGCACGGAACTGGC
-GACTCCACTGGGGTTGGGGTTTAGGGCAAGGAAGGAGAGGATCAGACCCTAATGTTGTTACGTGGGTTGG
-TCCGCATGTCAAGGAGAATCCAAGACACCCAATCCTTCACCTTGGCTGTGCCCCTAATCCTCATCTAAGC
-CAGGTTCAGATTCCAATCCTCTTTGGCCCAGTGCTCCGTGGGAAGCTCCCTCTGACCTTGGGCCTCAGCG
-CCTGGGGTTGCTGAGCCTTCCTAGTATAGGTGGTGACATCGTAGCCCCTGGGACCTGGATCCTGCCCAGT
-CTGCAGGCCATCATCTCCAAATGGGGCTGAGATGAGATGTGAGGAAAGAGGGGAGACAGTGGTTTGGAAA
-ACTGGACTGGTGGCTTTTTTGGGTTTCCAGAGGACTCATCTTCCTCTGCTTCTAGAATATTCCCACTCTC
-TCTTCCCTTTCCTCATTCTTCCTGGGTTATTTTTTTTTCCCTTTGCTGAATTCGAGCCCCATTCCCTCCA
-GCCTCTTTCCCTGTCTTATCTAGCCCAGTCCAGTTATATTCTCATAGGCAGAGGCAACAGATGCTCCAAA
-TTTTCTGAGGTCGGTTCCAACATCGCCACCCTCTAAAATCAGTGAAACATCCTAACTACATGCCTCATAG
-TCCTCCTGTTTCCAAAAACTGCAAAGATCTCCTGGTTACCCTGTATGCCCATCTTTGGGCTAGAAAATCC
-TCTCACCCTGTTAATAGTAAGACCCTGGTTTGTACAAACTGCCTCAAACACAGAGTTTAGGGGCTTTTCC
-CTTCTCTCCGCCAACCTCTGACAGGCAGAGTCTGAGGCCTGGCCTCCAGCTGCTGCGGGGAGCAGGTCTG
-GTAAAGAATCCTGTGCAGGTCAGTGGTATACAGGTCCTGTCAGGTGACAGCCTGGGCGAGAGACTGGAAA
-GTATCAGGATAACACGGCTGCCAGACGAACAACAAAACAACACTGAATTCACAAGGCGCATTCGAATCCT
-CTCTCAGTCCATTTGATCCTCAGTCACACAGCCGAGTAGACACTTTATCAACTCATTTAACAGAAAGGGA
-AAGTGAAGCCCAGAGCGAGGCCAGCAACGTGGCAGGTCACTCTGGTCATCTAGGGCCTGTTCCCAACTCT
-TTCACATGTGGGTCTCCAATATGTTCCCTCCTGTCCCAATCTCTGCCGGCCCTCAGGTACATCCCAGAGG
-GCATGCAGTGCTCATGTGGAATCGACTACTACACCCTCAAGCCGGAGGTCAACAACGAGTCCTTTGTCAT
-CTACATGTTCGTGGTCCACTTCACCATCCCTATGATTGTCATATTCTTTTGCTATGGACAGCTGGTCTTC
-ACCGTCAAGGAGGTAAGGTCATGTGTTGGGCACTGGGGACATGCACACTGAGTGAATGGAGCCCAGCTCC
-ATTCCCAGAGTTGCCACAGTCTGGACACCTGACCTTGTGTCCCTGCAGGCAGCTGCCCAGCAGCAGGAGT
-CAGCCACCACCCAGAAGGCCGAGAAGGAGGTCACCCGTATGGTCATCATCATGGTCATTGCTTTCCTAAT
-CTGTTGGCTGCCGTATGCCGGCGTGGCATTCTACATCTTCACCCACCAGGGCTCTAACTTTGGCCCCATC
-TTCATGACCCTCCCGGCATTCTTTGCCAAGTCGTCCTCCATCTACAACCCTGTCATCTATATCATGATGA
-ACAAGCAGGTGCCAGGTGGTAGGGAGGGAGGGTCTGGGTCCCCCAGGCTGCAGGCACTGCCCACAGAGGA
-CAAGCCACATCCTTGACTAGGCAGACCCCAGTCTTCCCATCTGCAAAATTAGGCAGGGGAGTTCGTCTCC
-CCCAGGCATCAGAGACATCGGGGAGAAATGCACATTTCTGGAGATGAATCAGCATCTCAGGGTGGGCCCA
-GGAACCTGCACTTCTAAAAACCATTCCACATGACTCTGAGGCTAGCATGAGAAGTGATGATCCACATGGT
-TCTGGAGGCCTGCTTTAAAAGTCAAGTGGTCAAAGTCCCAAGCCTGGGAACGGGATGGTGCCAGTCTCCA
-TTAAAGAGATCAAAAGGAGCTAGAAAGTCTTGTGATGAAAGATGAAGGGATAAAGCCGTCCTTTAACACA
-GATCAGTGATTTCTCTGCAGAATCCATGACCCAGTGGGAAAAAGTGGTCCCTGGAGTCAGGCATATTGGA
-TTCAAATCCTAGCTCTGCTATTTTCTAGCTATGTAACCTTGGGCAAGTCATCTCCCTTCTCTGTGCTTCA
-GTTTCTTCTTTCATAGAAAGGGTAAAATCCCAAACTCTTGGGTTAAATGAGATAACTTACATAGCCCTTG
-ATATGCAGAGGCATTATGGAATGTCGTTAGTGACAAAGTTCCCTTGGGTTTGGTCCCTGGTATCTCTGGA
-GTGAGATTGCATATGTTCCCTTCAGAGGGTCAGATTTGGGATGAGAGTGGAGGCTGCGAGGGCCTGAGTG
-GGAAGGGATTGGAGGCAAATCTCACCAACCATGTCAGTTTGCTACACACACTTTGGGTGGACCCTGACCC
-TGACTCATGCTTCTTGCCTTCCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCCAC
-TGGGTGACGATGAGGCCTCCACCACTGCCTC
-
->gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds
-GTGCCCTTCTCCAACAAGACGGGTGTGGTGCGCAGCCCCTTCGAGTACCCGCAGTACTACCTGGCTGAGC
-CCTGGCAGTTCTCCATGCTGGCTGCCTACATGTTTCTGCTGATCGTGCTCGGATTCCCCATCAACTTCCT
-CACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCT
-GTGGCCAACCTCTTCATGGTCTTTGGAGGCTTCACCACCACCCTGTATACCTCTATGCATGGATACTTCG
-TCTTCGGGGCCACGGGATGCAATCTGGAGGGCTTCTTTGCCACGCTGGGCGGTGAAATCGCCCTGTGGTC
-CCTGGTGGTCCTGGCCATCGAGCGGTATGTGGTGGTCTGCAAGCCCATGAGCAACTTCCGCTTTGGGGAG
-AACCACGCCATCATGGGCCTCGCCTTCACGTGGGTCATGGCACTGGCCTGCGCTGCACCCCCACTAGCCG
-GCTGGTCCAGGTACATCCCAGAGGGCATGCAGTGCTCGTGTGGGATTGACTACTACACGCTCAAACCGGA
-GGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTGTCATTTTC
-TTCTGCTACGGACAGCTGGTGTTCACAGTGAAGGAGGCGGCTGCCCAGCAGCAGGAGTCAGCCACCACCC
-AGAAGGCCGAGAAGGAAGTCACGCGCATGGTCATCATCATGGTCGTTGCGTTCCTAATCTGTTGGCTGCC
-CTACGCCAGCGTGGCATTCTACATCTTTACCCACCAGGGCTCTAACTTTGGCCCTGTCTTCATGACCATC
-CCGGCATTCTTCGCCAAGTCATCCTCCATCTACAACCCGGTCATCTATATCATGATGAACAAGCAGTTCC
-GGAACTGCATGCTCACCACCCTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAAGCATCCACCACTGC
-CTC
-
->gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds
-ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCT
-TCGAGGCGCCGCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCT
-GATCATGCTTGGCTTCCCCATCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACC
-CCCCTCAACTACATCCTGCTCAACCTGGCCGTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCA
-CCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCCGACGGGCTGCAACCTCGAGGGCTTCTTTGC
-CACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCGAGCGGTACGTAGTGGTGTGC
-AAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACCTGGGTCATGG
-CTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTG
-CGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTA
-CACTTCATCATCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTG
-CAGCCCAGCAGCAGGAGTCGGCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCAT
-GGTCATCGCTTTCCTCATATGCTGGCTGCCCTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGA
-TCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCTTTGCCAAGACGTCTGCCGTCTATAACCCCG
-TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACTCTCTGCTGTGGCAAGAACCC
-CCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA
-
->gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds
-CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCC
-ACTGGTGTAGTGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTC
-TGTCTGCCTACATGTTCTTCCTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCAT
-CGAACATAAGAAACTGAGGACCCCACTGAACTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATG
-GTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGCACGGCTACTTTGTCTTCGGCCCCACCGGCT
-GCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGGTGCCTCGTTGTCCTGGCCAT
-TGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGCCATCATGGGT
-GTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC
-CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTT
-TGTGATCTACATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTG
-GTGTGCACCGTCAAAGAGGCCGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGG
-TCACCCGCATGGTCGTCATCATGGTCATCTCCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTG
-GTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATCTTCATGACCATTCCATCCTTCTTTGCCAAG
-AGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTTCCGCCATTGCATGATCACCA
-CCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTAAAACTGAGGC
-TTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA
-AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACAC
-AACCATATAGGTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTAC
-AATATAGTCAACTTGATAGCAAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGT
-GAAATAAATTGCAA
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/rhodopsin_proteins.fasta
--- a/test-data/rhodopsin_proteins.fasta	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
->gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
-MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
-PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
-KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVV
-HFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG
-SNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA
-
->gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin
-MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRT
-PLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVC
-KPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVV
-HFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQG
-SEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTEASSVSSSQ
-VSPA
-
->gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]
-VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
-VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
-NHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF
-FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTL
-PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS
-
->gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus]
-VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
-VANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
-NHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF
-FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTI
-PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS
-
->gi|223523|prf||0811197A rhodopsin [Bos taurus]
-MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRT
-PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
-KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYTPHEETNNESFVIYMFVVH
-FIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGS
-DFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA
-
->gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster]
-MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRT
-PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVC
-KPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTC
-HFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQG
-STFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTEASSVSSSS
-VSPA
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/tblastn_four_human_vs_rhodopsin.html
--- a/test-data/tblastn_four_human_vs_rhodopsin.html	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,787 +0,0 @@
-<HTML>
-<TITLE>BLAST Search Results</TITLE>
-<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
-<PRE>
-
-<b>TBLASTN 2.2.25+</b>
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
-cds
-
-Length=1574
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
-rhodopsin (RHO) gene, exons 1 through 5 and partial cds
-
-Length=4301
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
-(RHO) mRNA, partial cds
-
-Length=983
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
-rhodopsin, complete cds
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
-OS=Homo sapiens GN=ERP44 PE=1 SV=1
-
-Length=406
-
-<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
-water form rod opsin, complete cds
-
-Length=1344
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.347    0.182    0.684 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 127710
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
-cds
-
-Length=1574
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
-rhodopsin (RHO) gene, exons 1 through 5 and partial cds
-
-Length=4301
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
-(RHO) mRNA, partial cds
-
-Length=983
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
-rhodopsin, complete cds
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
-GN=BMP2K PE=1 SV=2
-
-Length=1161
-
-<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
-water form rod opsin, complete cds
-
-Length=1344
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.334    0.170    0.615 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 370988
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
-cds
-
-Length=1574
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
-rhodopsin (RHO) gene, exons 1 through 5 and partial cds
-
-Length=4301
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
-(RHO) mRNA, partial cds
-
-Length=983
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
-rhodopsin, complete cds
-
-Length=1047
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
-SV=4
-
-Length=1382
-
-<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
-water form rod opsin, complete cds
-
-Length=1344
-
-
-***** No hits found *****
-
-
-
-Lambda     K      H
-   0.346    0.180    0.700 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 441350
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
-
-Length=1047
-
-<script src="blastResult.js"></script>
- Score =  732 bits (1689),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 336/348 (97%), Positives = 343/348 (99%), Gaps = 0/348 (0%)
- Frame = +1
-
-Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
-             MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
-Sbjct  1     MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  180
-
-Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
-             VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG
-Sbjct  181   VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG  360
-
-Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
-             GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP
-Sbjct  361   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP  540
-
-Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
-             EG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQES
-Sbjct  541   EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES  720
-
-Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
-             ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++I
-Sbjct  721   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSI  900
-
-Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA  348
-             YNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA
-Sbjct  901   YNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA  1044
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
-cds
-
-Length=1574
-
-<script src="blastResult.js"></script>
- Score =  646 bits (1489),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 290/342 (85%), Positives = 320/342 (94%), Gaps = 1/342 (0%)
- Frame = +3
-
-Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
-             MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLY
-Sbjct  42    MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLY  221
-
-Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
-             VT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLG
-Sbjct  222   VTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLG  401
-
-Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
-             GEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIP
-Sbjct  402   GEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIP  581
-
-Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
-             EG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQES
-Sbjct  582   EGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQES  761
-
-Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
-             ATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++I
-Sbjct  762   ATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSI  941
-
-Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE  341
-             YNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE
-Sbjct  942   YNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE  1067
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
-rhodopsin (RHO) gene, exons 1 through 5 and partial cds
-
-Length=4301
-
-<script src="blastResult.js"></script>
- Score =  151 bits (342),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
- Identities = 69/74 (94%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
- Frame = +3
-
-Query  239   ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA  298
-             ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS+
-Sbjct  3147  ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSS  3326
-
-Query  299   AIYNPVIYIMMNKQ  312
-             +IYNPVIYIMMNKQ
-Sbjct  3327  SIYNPVIYIMMNKQ  3368
-
-
- Score =  126 bits (284),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
- Identities = 54/59 (92%), Positives = 57/59 (97%), Gaps = 0/59 (0%)
- Frame = +2
-
-Query  177   RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA  235
-             RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +
-Sbjct  2855  RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS  3031
-
-
- Score =  229 bits (523),  Expect = 1e-64, Method: Compositional matrix adjust.
- Identities = 107/111 (97%), Positives = 109/111 (99%), Gaps = 0/111 (0%)
- Frame = +1
-
-Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
-            VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
-Sbjct  1    VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  180
-
-Query  71   PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG  121
-            PLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG
-Sbjct  181  PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG  333
-
-
- Score =  122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
- Identities = 55/59 (94%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
- Frame = +3
-
-Query  119   LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR  177
-             L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR
-Sbjct  1404  LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR  1580
-
-
- Score = 57.7 bits (125),  Expect = 6e-13, Method: Compositional matrix adjust.
- Identities = 23/26 (89%), Positives = 24/26 (93%), Gaps = 0/26 (0%)
- Frame = +1
-
-Query  312   QFRNCMLTTICCGKNPLGDDEASATV  337
-             QFRNCMLTT+CCGKNPLGDDEAS T 
-Sbjct  4222  QFRNCMLTTLCCGKNPLGDDEASTTA  4299
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
-(RHO) mRNA, partial cds
-
-Length=983
-
-<script src="blastResult.js"></script>
- Score =  658 bits (1517),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 310/326 (96%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
- Frame = +1
-
-Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
-            VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
-Sbjct  1    VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  180
-
-Query  71   PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVV  130
-            PLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVV
-Sbjct  181  PLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVV  360
-
-Query  131  LAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGID  190
-            LAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGID
-Sbjct  361  LAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGID  540
-
-Query  191  YYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV  250
-            YYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEV
-Sbjct  541  YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV  720
-
-Query  251  TRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMN  310
-            TRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMN
-Sbjct  721  TRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMN  900
-
-Query  311  KQFRNCMLTTICCGKNPLGDDEASAT  336
-            KQFRNCMLTT+CCGKNPLGDDEAS T
-Sbjct  901  KQFRNCMLTTLCCGKNPLGDDEASTT  978
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
-rhodopsin, complete cds
-
-Length=1047
-
-<script src="blastResult.js"></script>
- Score =  711 bits (1640),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 325/348 (94%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
- Frame = +1
-
-Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
-             MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLY
-Sbjct  1     MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY  180
-
-Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
-             VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG
-Sbjct  181   VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG  360
-
-Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
-             GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP
-Sbjct  361   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP  540
-
-Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
-             EG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQES
-Sbjct  541   EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES  720
-
-Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
-             ATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+
-Sbjct  721   ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV  900
-
-Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA  348
-             YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA
-Sbjct  901   YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA  1044
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
-
-Length=348
-
-<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
-water form rod opsin, complete cds
-
-Length=1344
-
-<script src="blastResult.js"></script>
- Score =  626 bits (1444),  Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 281/342 (83%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
- Frame = +2
-
-Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
-             MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLY
-Sbjct  23    MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLY  202
-
-Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
-             VT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLG
-Sbjct  203   VTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLG  382
-
-Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
-             GEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV  TW MALACA PPL GWSRYIP
-Sbjct  383   GEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIP  562
-
-Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
-             EGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES
-Sbjct  563   EGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQES  742
-
-Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
-              TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+
-Sbjct  743   ETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSAL  922
-
-Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE  341
-             YNP+IYI MNKQFR CM+TT+CCGKNP   +D ASAT SKTE
-Sbjct  923   YNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE  1048
-
-
-
-Lambda     K      H
-   0.351    0.182    0.707 
-
-Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
-
-Effective search space used: 109230
-
-
-
-
-Matrix: BLOSUM80
-Gap Penalties: Existence: 10, Extension: 1
-Neighboring words threshold: 14
-Window for multiple hits: 25
-</PRE>
-</BODY>
-</HTML>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/tblastn_four_human_vs_rhodopsin.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163782|ref|NM_001009242.1|	96.55	348	12	0	1	348	1	1044	0.0	 732
-sp|P08100|OPSD_HUMAN	gi|2734705|gb|U59921.1|BBU59921	84.80	342	51	1	1	341	42	1067	0.0	 646
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.24	74	5	0	239	312	3147	3368	1e-72	 151
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	91.53	59	5	0	177	235	2855	3031	1e-72	 126
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	96.40	111	4	0	11	121	1	333	1e-64	 229
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.22	59	4	0	119	177	1404	1580	1e-32	 122
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	88.46	26	3	0	312	337	4222	4299	6e-13	57.7
-sp|P08100|OPSD_HUMAN	gi|283855822|gb|GQ290312.1|	95.09	326	16	0	11	336	1	978	0.0	 658
-sp|P08100|OPSD_HUMAN	gi|18148870|dbj|AB062417.1|	93.39	348	23	0	1	348	1	1044	0.0	 711
-sp|P08100|OPSD_HUMAN	gi|12583664|dbj|AB043817.1|	82.16	342	60	1	1	341	23	1048	0.0	 626
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,722 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
-  <BlastOutput_query-len>406</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM80</Parameters_matrix>
-      <Parameters_expect>1e-10</Parameters_expect>
-      <Parameters_gap-open>10</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_1</Hit_id>
-          <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def>
-          <Hit_accession>Subject_1</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>732.392902459534</Hsp_bit-score>
-              <Hsp_score>1689</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_2</Hit_id>
-          <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def>
-          <Hit_accession>Subject_2</Hit_accession>
-          <Hit_len>1574</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>646.119739014374</Hsp_bit-score>
-              <Hsp_score>1489</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>42</Hsp_hit-from>
-              <Hsp_hit-to>1067</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>290</Hsp_identity>
-              <Hsp_positive>320</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_3</Hit_id>
-          <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def>
-          <Hit_accession>Subject_3</Hit_accession>
-          <Hit_len>4301</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>151.343146656381</Hsp_bit-score>
-              <Hsp_score>342</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>239</Hsp_query-from>
-              <Hsp_query-to>312</Hsp_query-to>
-              <Hsp_hit-from>3147</Hsp_hit-from>
-              <Hsp_hit-to>3368</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>69</Hsp_identity>
-              <Hsp_positive>73</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>74</Hsp_align-len>
-              <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq>
-              <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq>
-              <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>126.323929257285</Hsp_bit-score>
-              <Hsp_score>284</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>177</Hsp_query-from>
-              <Hsp_query-to>235</Hsp_query-to>
-              <Hsp_hit-from>2855</Hsp_hit-from>
-              <Hsp_hit-to>3031</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>54</Hsp_identity>
-              <Hsp_positive>57</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq>
-              <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq>
-              <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>229.420359574251</Hsp_bit-score>
-              <Hsp_score>523</Hsp_score>
-              <Hsp_evalue>9.84654801241353e-65</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>121</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>333</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>107</Hsp_identity>
-              <Hsp_positive>109</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>111</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>122.873002719478</Hsp_bit-score>
-              <Hsp_score>276</Hsp_score>
-              <Hsp_evalue>1.40732096096596e-32</Hsp_evalue>
-              <Hsp_query-from>119</Hsp_query-from>
-              <Hsp_query-to>177</Hsp_query-to>
-              <Hsp_hit-from>1404</Hsp_hit-from>
-              <Hsp_hit-to>1580</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>55</Hsp_identity>
-              <Hsp_positive>56</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq>
-              <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq>
-              <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>57.7367643183824</Hsp_bit-score>
-              <Hsp_score>125</Hsp_score>
-              <Hsp_evalue>5.60065526485586e-13</Hsp_evalue>
-              <Hsp_query-from>312</Hsp_query-from>
-              <Hsp_query-to>337</Hsp_query-to>
-              <Hsp_hit-from>4222</Hsp_hit-from>
-              <Hsp_hit-to>4299</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>23</Hsp_identity>
-              <Hsp_positive>24</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>26</Hsp_align-len>
-              <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq>
-              <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq>
-              <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>983</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>658.197981896696</Hsp_bit-score>
-              <Hsp_score>1517</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>336</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>978</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>310</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>326</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_5</Hit_id>
-          <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def>
-          <Hit_accession>Subject_5</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>711.255977415469</Hsp_bit-score>
-              <Hsp_score>1640</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>325</Hsp_identity>
-              <Hsp_positive>337</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_6</Hit_id>
-          <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def>
-          <Hit_accession>Subject_6</Hit_accession>
-          <Hit_len>1344</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>626.708277239213</Hsp_bit-score>
-              <Hsp_score>1444</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>23</Hsp_hit-from>
-              <Hsp_hit-to>1048</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>281</Hsp_identity>
-              <Hsp_positive>311</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163782|ref|NM_001009242.1|	96.55	348	12	0	1	348	1	1044	0.0	 732	gi|57163782|ref|NM_001009242.1|	1689	336	343	0	98.56	0	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	1047
-sp|P08100|OPSD_HUMAN	gi|2734705|gb|U59921.1|BBU59921	84.80	342	51	1	1	341	42	1067	0.0	 646	gi|2734705|gb|U59921.1|BBU59921	1489	290	320	1	93.57	0	3	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	1574
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.24	74	5	0	239	312	3147	3368	1e-72	 151	gi|283855845|gb|GQ290303.1|	342	69	73	0	98.65	0	3	ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ	ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ	348	4301
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	91.53	59	5	0	177	235	2855	3031	1e-72	 126	gi|283855845|gb|GQ290303.1|	284	54	57	0	96.61	0	2	RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA	RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS	348	4301
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	96.40	111	4	0	11	121	1	333	1e-64	 229	gi|283855845|gb|GQ290303.1|	523	107	109	0	98.20	0	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG	348	4301
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.22	59	4	0	119	177	1404	1580	1e-32	 122	gi|283855845|gb|GQ290303.1|	276	55	56	0	94.92	0	3	LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR	LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR	348	4301
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	88.46	26	3	0	312	337	4222	4299	6e-13	57.7	gi|283855845|gb|GQ290303.1|	125	23	24	0	92.31	0	1	QFRNCMLTTICCGKNPLGDDEASATV	QFRNCMLTTLCCGKNPLGDDEASTTA	348	4301
-sp|P08100|OPSD_HUMAN	gi|283855822|gb|GQ290312.1|	95.09	326	16	0	11	336	1	978	0.0	 658	gi|283855822|gb|GQ290312.1|	1517	310	322	0	98.77	0	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT	348	983
-sp|P08100|OPSD_HUMAN	gi|18148870|dbj|AB062417.1|	93.39	348	23	0	1	348	1	1044	0.0	 711	gi|18148870|dbj|AB062417.1|	1640	325	337	0	96.84	0	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	1047
-sp|P08100|OPSD_HUMAN	gi|12583664|dbj|AB043817.1|	82.16	342	60	1	1	341	23	1048	0.0	 626	gi|12583664|dbj|AB043817.1|	1444	281	311	1	90.94	0	2	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	1344
diff -r 45ba7c750bc8 -r 6ef523b390e0 test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-sp|P08100|OPSD_HUMAN	gi|57163782|ref|NM_001009242.1|	96.55	348	12	0	1	348	1	1044	0.0	 732
-sp|P08100|OPSD_HUMAN	gi|2734705|gb|U59921.1|BBU59921	84.80	342	51	1	1	341	42	1067	0.0	 646
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.24	74	5	0	239	312	3147	3368	1e-72	 151
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	91.53	59	5	0	177	235	2855	3031	1e-72	 126
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	96.40	111	4	0	11	121	1	333	1e-64	 229
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	93.22	59	4	0	119	177	1404	1580	1e-32	 122
-sp|P08100|OPSD_HUMAN	gi|283855845|gb|GQ290303.1|	88.46	26	3	0	312	337	4222	4299	6e-13	57.7
-sp|P08100|OPSD_HUMAN	gi|283855822|gb|GQ290312.1|	95.09	326	16	0	11	336	1	978	0.0	 658
-sp|P08100|OPSD_HUMAN	gi|18148870|dbj|AB062417.1|	93.39	348	23	0	1	348	1	1044	0.0	 711
-sp|P08100|OPSD_HUMAN	gi|12583664|dbj|AB043817.1|	82.16	342	60	1	1	341	23	1048	0.0	 626
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/blastdb.loc.sample
--- a/tools/ncbi_blast_plus/blastdb.loc.sample	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#This is a sample file distributed with Galaxy that is used to define a
-#list of nucleotide BLAST databases, using three columns tab separated
-#(longer whitespace are TAB characters):
-#
-#<unique_id>	<database_caption>	<base_name_path>
-#
-#The captions typically contain spaces and might end with the build date.
-#It is important that the actual database name does not have a space in it,
-#and that the first tab that appears in the line is right before the path.
-#
-#So, for example, if your database is nt and the path to your base name 
-#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry 
-#would look like this:
-#
-#nt_02_Dec_2009      nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
-#
-#and your /depot/data2/galaxy/blastdb/nt directory would contain all of 
-#your "base names" (e.g.):
-#
-#-rw-r--r--  1 wychung galaxy  23437408 2008-04-09 11:26 nt.chunk.00.nhr
-#-rw-r--r--  1 wychung galaxy   3689920 2008-04-09 11:26 nt.chunk.00.nin
-#-rw-r--r--  1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
-#...etc...
-#
-#Your blastdb.loc file should include an entry per line for each "base name" 
-#you have stored.  For example:
-#
-#nt_02_Dec_2009		nt 02 Dec 2009		/depot/data2/galaxy/blastdb/nt/nt.chunk
-#wgs_30_Nov_2009	wgs 30 Nov 2009	/depot/data2/galaxy/blastdb/wgs/wgs.chunk
-#test_20_Sep_2008	test 20 Sep 2008	/depot/data2/galaxy/blastdb/test/test
-#...etc...
-#
-#See also blastdb_p.loc which is for any protein BLAST database.
-#
-#Note that for backwards compatibility with workflows, the unique ID of
-#an entry must be the path that was in the original loc file, because that
-#is the value stored in the workflow for that parameter.
-#
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/blastdb_p.loc.sample
--- a/tools/ncbi_blast_plus/blastdb_p.loc.sample	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#This is a sample file distributed with Galaxy that is used to define a
-#list of protein BLAST databases, using three columns tab separated
-#(longer whitespace are TAB characters):
-#
-#<unique_id>	<database_caption>	<base_name_path>
-#
-#The captions typically contain spaces and might end with the build date.
-#It is important that the actual database name does not have a space in it,
-#and that the first tab that appears in the line is right before the path.
-#
-#So, for example, if your database is NR and the path to your base name
-#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
-#
-#nr		NCBI NR (non redundant)		/data/blastdb/nr
-#
-#and your /data/blastdb directory would contain all of the files associated
-#with the database, /data/blastdb/nr.*.
-#
-#Your blastdb_p.loc file should include an entry per line for each "base name"
-#you have stored. For example:
-#
-#nr_05Jun2010	NCBI NR (non redundant) 05 Jun 2010		/data/blastdb/05Jun2010/nr
-#nr_15Aug2010	NCBI NR (non redundant) 15 Aug 2010		/data/blastdb/15Aug2010/nr
-#...etc...
-#
-#See also blastdb.loc which is for any nucleotide BLAST database.
-#
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,254 +0,0 @@
-#!/usr/bin/env python
-"""Convert a BLAST XML file to 12 column tabular output
-
-Takes three command line options, input BLAST XML filename, output tabular
-BLAST filename, output format (std for standard 12 columns, or ext for the
-extended 24 columns offered in the BLAST+ wrappers).
-
-The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
-qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
-mean:
-   
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The additional columns offered in the Galaxy BLAST+ wrappers are:
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-Most of these fields are given explicitly in the XML file, others some like
-the percentage identity and the number of gap openings must be calculated.
-
-Be aware that the sequence in the extended tabular output or XML direct from
-BLAST+ may or may not use XXXX masking on regions of low complexity. This
-can throw the off the calculation of percentage identity and gap openings.
-[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
-with these numbers changing depending on whether or not the low complexity
-filter is used.]
-
-This script attempts to produce identical output to what BLAST+ would have done.
-However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
-space character (probably a bug).
-"""
-import sys
-import re
-
-if sys.version_info[:2] >= ( 2, 5 ):
-    import xml.etree.cElementTree as ElementTree
-else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
-    from elementtree import ElementTree
-
-def stop_err( msg ):
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(1)
-
-#Parse Command Line
-try:
-    in_file, out_file, out_fmt = sys.argv[1:]
-except:
-    stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
-
-if out_fmt == "std":
-    extended = False
-elif out_fmt == "x22":
-    stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
-elif out_fmt == "ext":
-    extended = True
-else:
-    stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
-
-
-# get an iterable
-try: 
-    context = ElementTree.iterparse(in_file, events=("start", "end"))
-except:
-    stop_err("Invalid data format.")
-# turn it into an iterator
-context = iter(context)
-# get the root element
-try:
-    event, root = context.next()
-except:
-    stop_err( "Invalid data format." )
-
-
-re_default_query_id = re.compile("^Query_\d+$")
-assert re_default_query_id.match("Query_101")
-assert not re_default_query_id.match("Query_101a")
-assert not re_default_query_id.match("MyQuery_101")
-re_default_subject_id = re.compile("^Subject_\d+$")
-assert re_default_subject_id.match("Subject_1")
-assert not re_default_subject_id.match("Subject_")
-assert not re_default_subject_id.match("Subject_12a")
-assert not re_default_subject_id.match("TheSubject_1")
-
-
-outfile = open(out_file, 'w')
-blast_program = None
-for event, elem in context:
-    if event == "end" and elem.tag == "BlastOutput_program":
-        blast_program = elem.text
-    # for every <Iteration> tag
-    if event == "end" and elem.tag == "Iteration":
-        #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
-        # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-        # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-        # <Iteration_query-len>406</Iteration_query-len>
-        # <Iteration_hits></Iteration_hits>
-        #
-        #Or, from BLAST 2.2.24+ run online
-        # <Iteration_query-ID>Query_1</Iteration_query-ID>
-        # <Iteration_query-def>Sample</Iteration_query-def>
-        # <Iteration_query-len>516</Iteration_query-len>
-        # <Iteration_hits>...
-        qseqid = elem.findtext("Iteration_query-ID")
-        if re_default_query_id.match(qseqid):
-            #Place holder ID, take the first word of the query definition
-            qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
-        qlen = int(elem.findtext("Iteration_query-len"))
-                                        
-        # for every <Hit> within <Iteration>
-        for hit in elem.findall("Iteration_hits/Hit"):
-            #Expecting either this,
-            # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-            # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-            # <Hit_accession>P56514</Hit_accession>
-            #or,
-            # <Hit_id>Subject_1</Hit_id>
-            # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
-            # <Hit_accession>Subject_1</Hit_accession>
-            #
-            #apparently depending on the parse_deflines switch
-            sseqid = hit.findtext("Hit_id").split(None,1)[0]
-            hit_def = sseqid + " " + hit.findtext("Hit_def")
-            if re_default_subject_id.match(sseqid) \
-            and sseqid == hit.findtext("Hit_accession"):
-                #Place holder ID, take the first word of the subject definition
-                hit_def = hit.findtext("Hit_def")
-                sseqid = hit_def.split(None,1)[0]
-            # for every <Hsp> within <Hit>
-            for hsp in hit.findall("Hit_hsps/Hsp"):
-                nident = hsp.findtext("Hsp_identity")
-                length = hsp.findtext("Hsp_align-len")
-                pident = "%0.2f" % (100*float(nident)/float(length))
-
-                q_seq = hsp.findtext("Hsp_qseq")
-                h_seq = hsp.findtext("Hsp_hseq")
-                m_seq = hsp.findtext("Hsp_midline")
-                assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
-                gapopen = str(len(q_seq.replace('-', ' ').split())-1  + \
-                              len(h_seq.replace('-', ' ').split())-1)
-
-                mismatch = m_seq.count(' ') + m_seq.count('+') \
-                         - q_seq.count('-') - h_seq.count('-')
-                #TODO - Remove this alternative mismatch calculation and test
-                #once satisifed there are no problems
-                expected_mismatch = len(q_seq) \
-                                  - sum(1 for q,h in zip(q_seq, h_seq) \
-                                        if q == h or q == "-" or h == "-")
-                xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
-                if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
-                    stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
-                                int(mismatch), expected_mismatch))
-
-                #TODO - Remove this alternative identity calculation and test
-                #once satisifed there are no problems
-                expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
-                if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
-                    stop_err("%s vs %s identities, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_identity, int(nident),
-                                expected_identity + q_seq.count("X")))
-                
-
-                evalue = hsp.findtext("Hsp_evalue")
-                if evalue == "0":
-                    evalue = "0.0"
-                else:
-                    evalue = "%0.0e" % float(evalue)
-                
-                bitscore = float(hsp.findtext("Hsp_bit-score"))
-                if bitscore < 100:
-                    #Seems to show one decimal place for lower scores
-                    bitscore = "%0.1f" % bitscore
-                else:
-                    #Note BLAST does not round to nearest int, it truncates
-                    bitscore = "%i" % bitscore
-
-                values = [qseqid,
-                          sseqid,
-                          pident,
-                          length, #hsp.findtext("Hsp_align-len")
-                          str(mismatch),
-                          gapopen,
-                          hsp.findtext("Hsp_query-from"), #qstart,
-                          hsp.findtext("Hsp_query-to"), #qend,
-                          hsp.findtext("Hsp_hit-from"), #sstart,
-                          hsp.findtext("Hsp_hit-to"), #send,
-                          evalue, #hsp.findtext("Hsp_evalue") in scientific notation
-                          bitscore, #hsp.findtext("Hsp_bit-score") rounded
-                          ]
-
-                if extended:
-                    sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
-                    #print hit_def, "-->", sallseqid
-                    positive = hsp.findtext("Hsp_positive")
-                    ppos = "%0.2f" % (100*float(positive)/float(length))
-                    qframe = hsp.findtext("Hsp_query-frame")
-                    sframe = hsp.findtext("Hsp_hit-frame")
-                    if blast_program == "blastp":
-                        #Probably a bug in BLASTP that they use 0 or 1 depending on format
-                        if qframe == "0": qframe = "1"
-                        if sframe == "0": sframe = "1"
-                    slen = int(hit.findtext("Hit_len"))
-                    values.extend([sallseqid,
-                                   hsp.findtext("Hsp_score"), #score,
-                                   nident,
-                                   positive,
-                                   hsp.findtext("Hsp_gaps"), #gaps,
-                                   ppos,
-                                   qframe,
-                                   sframe,
-                                   #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
-                                   q_seq,
-                                   h_seq,
-                                   str(qlen),
-                                   str(slen),
-                                   ])
-                #print "\t".join(values) 
-                outfile.write("\t".join(values) + "\n")
-        # prevents ElementTree from growing large datastructure
-        root.clear()
-        elem.clear()
-outfile.close()
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
-    <description>Convert BLAST XML output to tabular</description>
-    <command interpreter="python">
-      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
-    </command>
-    <inputs>
-        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
-        <param name="out_format" type="select" label="Output format">
-            <option value="std" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
-    </outputs>
-    <requirements>
-    </requirements>
-    <tests>
-        <test>
-            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
-            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
-            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-**What it does**
-
-NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
-formats including tabular and a more detailed XML format. A complex workflow
-may need both the XML and the tabular output - but running BLAST twice is
-slow and wasteful.
-
-This tool takes the BLAST XML output and by default converts it into the
-standard 12 column tabular equivalent:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-Beware that the XML file (and thus the conversion) and the tabular output
-direct from BLAST+ may differ in the presence of XXXX masking on regions
-low complexity (columns 21 and 22), and thus also calculated figures like
-the percentage idenity (column 3).
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_blast_plus.txt
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-Galaxy wrappers for NCBI BLAST+ suite
-=====================================
-
-These wrappers are copyright 2010-2012 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+),
-and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall).
-
-Note that these wrappers (and the associated datetypes) were originally
-distributed as part of the main Galaxy repository, but as of August 2012
-moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes').
-My thanks to Dannon Baker from the Galaxy development team for his assistance
-with this.
-
-
-Manual Installation
-===================
-
-For those not using Galaxy's automated installation from the Tool Shed, put
-the XML and Python files under tools/ncbi_blast_plus and add the XML files
-to your tool_conf.xml as normal.
-
-You must tell Galaxy about any system level BLAST databases using configuration
-files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein
-databases like NR).
-
-You will also need to install 'blast_datatypes' from the Tool Shed. This
-defines the BLAST XML file format ('blastxml').
-
-
-History
-=======
-
-v0.0.11 - Final revision as part of the Galaxy main repository, and the
-          first release via the Tool Shed
-v0.0.12 - Implements genetic code option for translation searches.
-        - Changes <parallelism> to 1000 sequences at a time (to cope with
-          very large sets of queries where BLAST+ can become memory hungry)
-        - Include warning that BLAST+ with subject FASTA gives pairwise
-          e-values
-v0.0.13 - Use the new error handling options in Galaxy (the previously
-          bundled hide_stderr.py script is no longer needed).
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy root folder:
-
-$ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh
-
-This similifies ensuring a consistent set of files is bundled each time,
-including all the relevant test files.
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
-NOTE: This is the licence for the Galaxy Wrapper only. BLAST+ and
-associated data files are available and licenced separately.
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,215 +0,0 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.13">
-    <description>Search nucleotide database with nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into parts -->
-    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastn -version</version_command>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <stdio>
-        <exit_code range="1:" />
-	<exit_code range="://0" />
-    </stdio>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file (pairwise e-values)</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
-            <option value="megablast">megablast</option>
-            <option value="blastn">blastn</option>
-            <option value="blastn-short">blastn-short</option>
-            <option value="dc-megablast">dc-megablast</option>
-            <!-- Using BLAST 2.2.24+ this gives an error:
-            BLAST engine error: Program type 'vecscreen' not supported
-            <option value="vecscreen">vecscreen</option>
-            -->
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastn</requirement>
-    </requirements>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *nucleotide database* using a *nucleotide query*,
-using the NCBI BLAST+ blastn command line tool.
-Algorithms include blastn, megablast, and discontiguous megablast.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,282 +0,0 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.13">
-    <description>Search protein database with protein query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into parts -->
-    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastp -version</version_command>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastp
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <stdio>
-        <exit_code range="1:" />
-	<exit_code range="://0" />
-    </stdio>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file (pairwise e-values)</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Protein BLAST database">
-                    <options from_file="blastdb_p.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
-            <option value="blastp">blastp</option>
-            <option value="blastp-short">blastp-short</option>
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!--
-                Can't use '-ungapped' on its own, error back is:
-                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
-                Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
-                -->
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastp</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *protein database* using a *protein query*,
-using the NCBI BLAST+ blastp command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,268 +0,0 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.13">
-    <description>Search protein database with translated nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into parts -->
-    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastx -version</version_command>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--query_gencode $query_gencode
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range="://0" />
-    </stdio>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file (pairwise e-values)</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Protein BLAST database">
-                    <options from_file="blastdb_p.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="query_gencode" type="select" label="Query genetic code">
-            <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-            <option value="1" select="True">1. Standard</option>
-            <option value="2">2. Vertebrate Mitochondrial</option>
-            <option value="3">3. Yeast Mitochondrial</option>
-            <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-            <option value="5">5. Invertebrate Mitochondrial</option>
-            <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-            <option value="9">9. Echinoderm Mitochondrial</option>
-            <option value="10">10. Euplotid Nuclear</option>
-            <option value="11">11. Bacteria and Archaea</option>
-            <option value="12">12. Alternative Yeast Nuclear</option>         
-            <option value="13">13. Ascidian Mitochondrial</option>
-            <option value="14">14. Flatworm Mitochondrial</option>
-            <option value="15">15. Blepharisma Macronuclear</option>
-            <option value="16">16. Chlorophycean Mitochondrial Code</option>
-            <option value="21">21. Trematode Mitochondrial Code</option>
-            <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
-            <option value="23">23. Thraustochytrium Mitochondrial Code</option>
-            <option value="24">24. Pterobranchia mitochondrial code</option>
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastx -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastx</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *protein database* using a *translated nucleotide query*,
-using the NCBI BLAST+ blastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length 
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,314 +0,0 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.13">
-    <description>Search translated nucleotide database with protein query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into parts -->
-    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>tblastn -version</version_command>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
--db_gencode $adv_opts.db_gencode
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range="://0" />
-    </stdio>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file (pairwise e-values)</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <param name="db_gencode" type="select" label="Database/subject genetic code">
-                    <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-                    <option value="1" select="True">1. Standard</option>
-                    <option value="2">2. Vertebrate Mitochondrial</option>
-                    <option value="3">3. Yeast Mitochondrial</option>
-                    <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-                    <option value="5">5. Invertebrate Mitochondrial</option>
-                    <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-                    <option value="9">9. Echinoderm Mitochondrial</option>
-                    <option value="10">10. Euplotid Nuclear</option>
-                    <option value="11">11. Bacteria and Archaea</option>
-                    <option value="12">12. Alternative Yeast Nuclear</option>
-                    <option value="13">13. Ascidian Mitochondrial</option>
-                    <option value="14">14. Flatworm Mitochondrial</option>
-                    <option value="15">15. Blepharisma Macronuclear</option>
-                    <option value="16">16. Chlorophycean Mitochondrial Code</option>
-                    <option value="21">21. Trematode Mitochondrial Code</option>
-                    <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
-                    <option value="23">23. Thraustochytrium Mitochondrial Code</option>
-                    <option value="24">24. Pterobranchia mitochondrial code</option>
-                </param>
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!--
-                Can't use '-ungapped' on its own, error back is:
-                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
-                Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
-                -->
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">tblastn</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="true" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="0 -html" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastn command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,256 +0,0 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.13">
-    <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into parts -->
-    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>tblastx -version</version_command>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--query_gencode $query_gencode
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
--db_gencode $adv_opts.db_gencode
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range="://0" />
-    </stdio>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file (pairwise e-values)</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="query_gencode" type="select" label="Query genetic code">
-            <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-            <option value="1" select="True">1. Standard</option>
-            <option value="2">2. Vertebrate Mitochondrial</option>
-            <option value="3">3. Yeast Mitochondrial</option>
-            <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-            <option value="5">5. Invertebrate Mitochondrial</option>
-            <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-            <option value="9">9. Echinoderm Mitochondrial</option>
-            <option value="10">10. Euplotid Nuclear</option>
-            <option value="11">11. Bacteria and Archaea</option>
-            <option value="12">12. Alternative Yeast Nuclear</option>
-            <option value="13">13. Ascidian Mitochondrial</option>
-            <option value="14">14. Flatworm Mitochondrial</option>
-            <option value="15">15. Blepharisma Macronuclear</option>
-            <option value="16">16. Chlorophycean Mitochondrial Code</option>
-            <option value="21">21. Trematode Mitochondrial Code</option>
-            <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
-            <option value="23">23. Thraustochytrium Mitochondrial Code</option>
-            <option value="24">24. Pterobranchia mitochondrial code</option>
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <param name="db_gencode" type="select" label="Database/subject genetic code">
-                    <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-                    <option value="1" select="True">1. Standard</option>
-                    <option value="2">2. Vertebrate Mitochondrial</option>
-                    <option value="3">3. Yeast Mitochondrial</option>
-                    <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-                    <option value="5">5. Invertebrate Mitochondrial</option>
-                    <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-                    <option value="9">9. Echinoderm Mitochondrial</option>
-                    <option value="10">10. Euplotid Nuclear</option>
-                    <option value="11">11. Bacteria and Archaea</option>
-                    <option value="12">12. Alternative Yeast Nuclear</option>
-                    <option value="13">13. Ascidian Mitochondrial</option>
-                    <option value="14">14. Flatworm Mitochondrial</option>
-                    <option value="15">15. Blepharisma Macronuclear</option>
-                    <option value="16">16. Chlorophycean Mitochondrial Code</option>
-                    <option value="21">21. Trematode Mitochondrial Code</option>
-                    <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
-                    <option value="23">23. Thraustochytrium Mitochondrial Code</option>
-                    <option value="24">24. Pterobranchia mitochondrial code</option>
-                </param>
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">tblastx</requirement>
-    </requirements>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>
diff -r 45ba7c750bc8 -r 6ef523b390e0 tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml	Thu Sep 20 10:12:43 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="blast+" version="2.2.26+">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action>
-                <action type="shell_command">cd c++ &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-These links provide information for building the NCBI Blast+ package in most environments.
-
-System requirements
-http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
-        </readme>
-    </package>
-</tool_dependency>
-