Mercurial > repos > devteam > ncbi_blast_plus

changeset 8:1f546099212f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
author peterjc
date Tue, 19 Feb 2013 12:49:43 -0500
parents 4ce66a5401d0
children 9dabbfd73c8a
files test-data/blastp_four_human_vs_rhodopsin.tabular test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_ext.tabular test-data/blastp_rhodopsin_vs_four_human.tabular test-data/blastx_rhodopsin_vs_four_human.tabular test-data/blastx_rhodopsin_vs_four_human.xml test-data/blastx_rhodopsin_vs_four_human_ext.tabular test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.tabular test-data/tblastn_four_human_vs_rhodopsin.xml test-data/tblastn_four_human_vs_rhodopsin_ext.tabular test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blast_plus.txt tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
diffstat 19 files changed, 140 insertions(+), 121 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/blastp_four_human_vs_rhodopsin.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastp_four_human_vs_rhodopsin.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -3,4 +3,4 @@
 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
+sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	0.0	 599
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.2.26+</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>
@@ -375,7 +375,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>701.049065538619</Hsp_bit-score>
+              <Hsp_bit-score>701.049</Hsp_bit-score>
               <Hsp_score>1808</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -422,7 +422,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>619.001555868222</Hsp_bit-score>
+              <Hsp_bit-score>619.002</Hsp_bit-score>
               <Hsp_score>1595</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -469,7 +469,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>653.284318124867</Hsp_bit-score>
+              <Hsp_bit-score>653.284</Hsp_bit-score>
               <Hsp_score>1684</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -516,7 +516,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>631.327942297578</Hsp_bit-score>
+              <Hsp_bit-score>631.328</Hsp_bit-score>
               <Hsp_score>1627</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -563,7 +563,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>673.314696072569</Hsp_bit-score>
+              <Hsp_bit-score>673.315</Hsp_bit-score>
               <Hsp_score>1736</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -610,9 +610,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>599.356377496438</Hsp_bit-score>
+              <Hsp_bit-score>599.356</Hsp_bit-score>
               <Hsp_score>1544</Hsp_score>
-              <Hsp_evalue>3.49521227372659e-176</Hsp_evalue>
+              <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>
@@ -643,4 +643,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -3,4 +3,4 @@
 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
+sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	0.0	 599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354
--- a/test-data/blastp_rhodopsin_vs_four_human.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastp_rhodopsin_vs_four_human.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -1,6 +1,6 @@
 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|3024260|sp|P56514.1|OPSD_BUFBU	sp|P08100|OPSD_HUMAN	83.33	354	53	2	1	354	1	348	0.0	 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
+gi|12583665|dbj|BAB21486.1|	sp|P08100|OPSD_HUMAN	81.09	349	65	1	1	349	1	348	0.0	 587
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastx_rhodopsin_vs_four_human.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -1,10 +1,10 @@
 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|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	0.0	 575
+gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.40	111	4	0	1	333	11	121	2e-68	 224
+gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.31	65	5	0	3174	3368	248	312	5e-36	 129
+gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	96.43	56	2	0	2855	3022	177	232	3e-33	 120
+gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	93.22	59	4	0	1404	1580	119	177	2e-32	 118
+gi|283855845|gb|GQ290303.1|	sp|P08100|OPSD_HUMAN	92.00	25	2	0	4222	4296	312	336	2e-12	56.2
+gi|283855822|gb|GQ290312.1|	sp|P08100|OPSD_HUMAN	95.09	326	16	0	1	978	11	336	0.0	 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
+gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	0.0	 559
--- a/test-data/blastx_rhodopsin_vs_four_human.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastx_rhodopsin_vs_four_human.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastx</BlastOutput_program>
-  <BlastOutput_version>BLASTX 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>BLASTX 2.2.26+</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>
@@ -90,7 +90,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>662.143908370966</Hsp_bit-score>
+              <Hsp_bit-score>662.144</Hsp_bit-score>
               <Hsp_score>1707</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -194,9 +194,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>575.088804213644</Hsp_bit-score>
+              <Hsp_bit-score>575.089</Hsp_bit-score>
               <Hsp_score>1481</Hsp_score>
-              <Hsp_evalue>1.31349806431671e-168</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>42</Hsp_query-from>
               <Hsp_query-to>1037</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -298,9 +298,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>224.171990552935</Hsp_bit-score>
+              <Hsp_bit-score>224.172</Hsp_bit-score>
               <Hsp_score>570</Hsp_score>
-              <Hsp_evalue>1.57574304751949e-62</Hsp_evalue>
+              <Hsp_evalue>1.84906e-68</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>333</Hsp_query-to>
               <Hsp_hit-from>11</Hsp_hit-from>
@@ -317,9 +317,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>129.412894877266</Hsp_bit-score>
+              <Hsp_bit-score>129.413</Hsp_bit-score>
               <Hsp_score>324</Hsp_score>
-              <Hsp_evalue>5.28220874623366e-34</Hsp_evalue>
+              <Hsp_evalue>4.62305e-36</Hsp_evalue>
               <Hsp_query-from>3174</Hsp_query-from>
               <Hsp_query-to>3368</Hsp_query-to>
               <Hsp_hit-from>248</Hsp_hit-from>
@@ -336,9 +336,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>120.938504207085</Hsp_bit-score>
+              <Hsp_bit-score>120.939</Hsp_bit-score>
               <Hsp_score>302</Hsp_score>
-              <Hsp_evalue>1.87871691987854e-31</Hsp_evalue>
+              <Hsp_evalue>2.85192e-33</Hsp_evalue>
               <Hsp_query-from>2855</Hsp_query-from>
               <Hsp_query-to>3022</Hsp_query-to>
               <Hsp_hit-from>177</Hsp_hit-from>
@@ -355,9 +355,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>118.242107175663</Hsp_bit-score>
+              <Hsp_bit-score>118.242</Hsp_bit-score>
               <Hsp_score>295</Hsp_score>
-              <Hsp_evalue>1.21774886471054e-30</Hsp_evalue>
+              <Hsp_evalue>2.16231e-32</Hsp_evalue>
               <Hsp_query-from>1404</Hsp_query-from>
               <Hsp_query-to>1580</Hsp_query-to>
               <Hsp_hit-from>119</Hsp_hit-from>
@@ -374,9 +374,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>56.2249754529693</Hsp_bit-score>
+              <Hsp_bit-score>56.225</Hsp_bit-score>
               <Hsp_score>134</Hsp_score>
-              <Hsp_evalue>5.68296036241677e-12</Hsp_evalue>
+              <Hsp_evalue>2.05678e-12</Hsp_evalue>
               <Hsp_query-from>4222</Hsp_query-from>
               <Hsp_query-to>4296</Hsp_query-to>
               <Hsp_hit-from>312</Hsp_hit-from>
@@ -478,9 +478,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>613.993961381297</Hsp_bit-score>
+              <Hsp_bit-score>613.994</Hsp_bit-score>
               <Hsp_score>1582</Hsp_score>
-              <Hsp_evalue>1.57028732393616e-180</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>978</Hsp_query-to>
               <Hsp_hit-from>11</Hsp_hit-from>
@@ -582,7 +582,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>641.728330847346</Hsp_bit-score>
+              <Hsp_bit-score>641.728</Hsp_bit-score>
               <Hsp_score>1654</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -686,9 +686,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>559.295621601033</Hsp_bit-score>
+              <Hsp_bit-score>559.296</Hsp_bit-score>
               <Hsp_score>1440</Hsp_score>
-              <Hsp_evalue>6.32632556748138e-164</Hsp_evalue>
+              <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>23</Hsp_query-from>
               <Hsp_query-to>1018</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -719,4 +719,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -1,10 +1,10 @@
 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|2734705|gb|U59921.1|BBU59921	sp|P08100|OPSD_HUMAN	85.24	332	49	0	42	1037	1	332	0.0	 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-68	 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-36	 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	3e-33	 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	2e-32	 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	2e-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	0.0	 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
+gi|12583664|dbj|AB043817.1|	sp|P08100|OPSD_HUMAN	81.93	332	60	0	23	1018	1	332	0.0	 559	sp|P08100|OPSD_HUMAN	1440	272	307	0	92.47	2	0	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE	1344	348
--- a/test-data/tblastn_four_human_vs_rhodopsin.html	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.html	Tue Feb 19 12:49:43 2013 -0500
@@ -3,7 +3,7 @@
 <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
 <PRE>
 
-<b>TBLASTN 2.2.25+</b>
+<b>TBLASTN 2.2.26+</b>
 
 
 <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
@@ -563,7 +563,7 @@
 
 <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%)
+ Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
  Frame = +3
 
 Query  239   ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA  298
@@ -584,8 +584,8 @@
 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%)
+ Score =  229 bits (523),  Expect = 9e-67, Method: Compositional matrix adjust.
+ Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%)
  Frame = +1
 
 Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
@@ -598,7 +598,7 @@
 
 
  Score =  122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
- Identities = 55/59 (94%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
+ Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
  Frame = +3
 
 Query  119   LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR  177
@@ -606,8 +606,8 @@
 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%)
+ Score = 57.7 bits (125),  Expect = 2e-12, Method: Compositional matrix adjust.
+ Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%)
  Frame = +1
 
 Query  312   QFRNCMLTTICCGKNPLGDDEASATV  337
@@ -637,7 +637,7 @@
 
 <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%)
+ Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
  Frame = +1
 
 Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
@@ -687,7 +687,7 @@
 
 <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%)
+ Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
  Frame = +1
 
 Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
@@ -737,7 +737,7 @@
 
 <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%)
+ Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
  Frame = +2
 
 Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -2,9 +2,9 @@
 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|	96.40	111	4	0	11	121	1	333	9e-67	 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|283855845|gb|GQ290303.1|	88.46	26	3	0	312	337	4222	4299	2e-12	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
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
+  <BlastOutput_version>TBLASTN 2.2.26+</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>
@@ -375,7 +375,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>732.392902459534</Hsp_bit-score>
+              <Hsp_bit-score>732.393</Hsp_bit-score>
               <Hsp_score>1689</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -422,7 +422,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>646.119739014374</Hsp_bit-score>
+              <Hsp_bit-score>646.12</Hsp_bit-score>
               <Hsp_score>1489</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -469,9 +469,9 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>151.343146656381</Hsp_bit-score>
+              <Hsp_bit-score>151.343</Hsp_bit-score>
               <Hsp_score>342</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
+              <Hsp_evalue>1.39567e-72</Hsp_evalue>
               <Hsp_query-from>239</Hsp_query-from>
               <Hsp_query-to>312</Hsp_query-to>
               <Hsp_hit-from>3147</Hsp_hit-from>
@@ -488,9 +488,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>126.323929257285</Hsp_bit-score>
+              <Hsp_bit-score>126.324</Hsp_bit-score>
               <Hsp_score>284</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
+              <Hsp_evalue>1.39567e-72</Hsp_evalue>
               <Hsp_query-from>177</Hsp_query-from>
               <Hsp_query-to>235</Hsp_query-to>
               <Hsp_hit-from>2855</Hsp_hit-from>
@@ -507,9 +507,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>229.420359574251</Hsp_bit-score>
+              <Hsp_bit-score>229.42</Hsp_bit-score>
               <Hsp_score>523</Hsp_score>
-              <Hsp_evalue>9.84654801241353e-65</Hsp_evalue>
+              <Hsp_evalue>9.34154e-67</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
               <Hsp_query-to>121</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
@@ -526,9 +526,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>122.873002719478</Hsp_bit-score>
+              <Hsp_bit-score>122.873</Hsp_bit-score>
               <Hsp_score>276</Hsp_score>
-              <Hsp_evalue>1.40732096096596e-32</Hsp_evalue>
+              <Hsp_evalue>1.03783e-32</Hsp_evalue>
               <Hsp_query-from>119</Hsp_query-from>
               <Hsp_query-to>177</Hsp_query-to>
               <Hsp_hit-from>1404</Hsp_hit-from>
@@ -545,9 +545,9 @@
             </Hsp>
             <Hsp>
               <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>57.7367643183824</Hsp_bit-score>
+              <Hsp_bit-score>57.7368</Hsp_bit-score>
               <Hsp_score>125</Hsp_score>
-              <Hsp_evalue>5.60065526485586e-13</Hsp_evalue>
+              <Hsp_evalue>1.50808e-12</Hsp_evalue>
               <Hsp_query-from>312</Hsp_query-from>
               <Hsp_query-to>337</Hsp_query-to>
               <Hsp_hit-from>4222</Hsp_hit-from>
@@ -592,7 +592,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>658.197981896696</Hsp_bit-score>
+              <Hsp_bit-score>658.198</Hsp_bit-score>
               <Hsp_score>1517</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>11</Hsp_query-from>
@@ -639,7 +639,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>711.255977415469</Hsp_bit-score>
+              <Hsp_bit-score>711.256</Hsp_bit-score>
               <Hsp_score>1640</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -686,7 +686,7 @@
           <Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>626.708277239213</Hsp_bit-score>
+              <Hsp_bit-score>626.708</Hsp_bit-score>
               <Hsp_score>1444</Hsp_score>
               <Hsp_evalue>0</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
@@ -719,4 +719,4 @@
       </Iteration_stat>
     </Iteration>
   </BlastOutput_iterations>
-</BlastOutput>
+</BlastOutput>
\ No newline at end of file
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular	Tue Feb 19 12:49:43 2013 -0500
@@ -2,9 +2,9 @@
 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|	96.40	111	4	0	11	121	1	333	9e-67	 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|283855845|gb|GQ290303.1|	88.46	26	3	0	312	337	4222	4299	2e-12	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
--- a/test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular	Fri Feb 08 05:51:26 2013 -0500
+++ /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
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,13 +1,18 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10">
     <description>Convert BLAST XML output to tabular</description>
     <command interpreter="python">
       blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
     </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <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>
+            <option value="std">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
         </param>
     </inputs>
     <outputs>
@@ -74,7 +79,7 @@
 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
+This tool takes the BLAST XML output and can convert it into the
 standard 12 column tabular equivalent:
 
 ====== ========= ============================================
@@ -99,7 +104,7 @@
 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.
+BLAST output. This tool now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
@@ -121,7 +126,7 @@
 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).
+the percentage identity (column 3).
 
     </help>
 </tool>
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Tue Feb 19 12:49:43 2013 -0500
@@ -34,7 +34,20 @@
 
 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.
+to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample
+in order to run the unit tests). For example, use:
+
+  <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
+    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />
+    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
+  </section>
 
 You will also need to install 'blast_datatypes' from the Tool Shed. This
 defines the BLAST XML file format ('blastxml') and protein and nucleotide
@@ -45,6 +58,14 @@
 databases like NR), located in the tool-data folder. Sample fils are included
 which explain the tab based format to use.
 
+You must install the NCBI BLAST+ standalone tools somewhere on the system
+path. Currently the unit tests are written using "BLAST 2.2.26+".
+
+Run the functional tests (adusting the section identifier to match your
+tool_conf.xml.sample file):
+
+./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
+
 
 History
 =======
@@ -65,6 +86,9 @@
           FASTA files (better looking e-values than you might be expecting).
 v0.0.16 - Added repository_dependencies.xml for automates installation of the
           'blast_datatypes' repository from the Tool Shed.
+v0.0.17 - The BLAST+ search tools now default to extended tabular output
+          (all too often our users where having to re-run searches just to
+          get one of the missing columns like query or subject length)
 
 
 Developers
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.15">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.17">
     <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,histdb" merge_outputs="output1"></parallelism>
@@ -91,8 +91,8 @@
         </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="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -200,7 +200,7 @@
 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.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.15">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.17">
     <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,histdb" merge_outputs="output1"></parallelism>
@@ -86,8 +86,8 @@
         </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="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -265,7 +265,7 @@
 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.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.15">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.17">
     <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,histdb" merge_outputs="output1"></parallelism>
@@ -103,8 +103,8 @@
         </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="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -253,7 +253,7 @@
 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.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.15">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.17">
     <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,histdb" merge_outputs="output1"></parallelism>
@@ -82,8 +82,8 @@
         </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="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -216,7 +216,7 @@
             <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 -->
+            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ - 2.2.27+ 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" />
@@ -299,7 +299,7 @@
 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.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Feb 19 12:49:43 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.15">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.17">
     <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,histdb" merge_outputs="output1"></parallelism>
@@ -103,8 +103,8 @@
         </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="6">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
             <option value="5">BLAST XML</option>
             <option value="0">Pairwise text</option>
             <option value="0 -html">Pairwise HTML</option>
@@ -241,7 +241,7 @@
 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.
+BLAST output. Galaxy now uses this extended 24 column output by default.
 
 ====== ============= ===========================================
 Column NCBI name     Description