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diff test-data/blastxml/blast-gene1.xml @ 3:7342f467507b draft

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastxml/blast-gene1.xml	Thu Dec 31 13:58:43 2015 -0500
@@ -0,0 +1,126 @@
+<?xml version="1.0"?>
+<!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 2.2.28+</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>/usr/local/syncdb/community/nr/nr</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>Merlin_1</BlastOutput_query-def>
+  <BlastOutput_query-len>229</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>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>Merlin_1</Iteration_query-def>
+  <Iteration_query-len>229</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|422934611|ref|YP_007004572.1|</Hit_id>
+  <Hit_def>hypothetical protein [Enterobacteria phage ime09] &gt;gi|339791394|gb|AEK12451.1| hypothetical protein [Enterobacteria phage ime09]</Hit_def>
+  <Hit_accession>YP_007004572</Hit_accession>
+  <Hit_len>685</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>197.593</Hsp_bit-score>
+      <Hsp_score>501</Hsp_score>
+      <Hsp_evalue>3.74548e-55</Hsp_evalue>
+      <Hsp_query-from>2</Hsp_query-from>
+      <Hsp_query-to>229</Hsp_query-to>
+      <Hsp_hit-from>474</Hsp_hit-from>
+      <Hsp_hit-to>684</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>106</Hsp_identity>
+      <Hsp_positive>154</Hsp_positive>
+      <Hsp_gaps>21</Hsp_gaps>
+      <Hsp_align-len>230</Hsp_align-len>
+      <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
+      <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGSHSAYANED-----------AETSVGMVIKGAERIKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYMMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
+      <Hsp_midline>L  GT LYRGQ++   T  HN ENK+FYF+N+VSTSLKP IFGE G+ +MALDD   +++ E         + ED++ +G+    + +D            + ++G VI GAE ++VIVPG L+ +P EAEVILPRG LLKINK++T + K +  NK+++EG+IVPPSEQ++ESV  YDGD  METGEV  ++GF QF+ E +  +E+    ++IL+  ++I+ M +KF+</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+<Hit>
+  <Hit_num>2</Hit_num>
+  <Hit_id>gi|330858714|ref|YP_004415089.1|</Hit_id>
+  <Hit_def>hypothetical protein Shfl2p198 [Shigella phage Shfl2] &gt;gi|327397648|gb|AEA73150.1| hypothetical protein Shfl2p198 [Shigella phage Shfl2]</Hit_def>
+  <Hit_accession>YP_004415089</Hit_accession>
+  <Hit_len>685</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>197.593</Hsp_bit-score>
+      <Hsp_score>501</Hsp_score>
+      <Hsp_evalue>4.31042e-55</Hsp_evalue>
+      <Hsp_query-from>2</Hsp_query-from>
+      <Hsp_query-to>229</Hsp_query-to>
+      <Hsp_hit-from>474</Hsp_hit-from>
+      <Hsp_hit-to>684</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>106</Hsp_identity>
+      <Hsp_positive>154</Hsp_positive>
+      <Hsp_gaps>21</Hsp_gaps>
+      <Hsp_align-len>230</Hsp_align-len>
+      <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
+      <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGSHSAYANED-----------AETSVGMVIKGAERIKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYMMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
+      <Hsp_midline>L  GT LYRGQ++   T  HN ENK+FYF+N+VSTSLKP IFGE G+ +MALDD   +++ E         + ED++ +G+    + +D            + ++G VI GAE ++VIVPG L+ +P EAEVILPRG LLKINK++T + K +  NK+++EG+IVPPSEQ++ESV  YDGD  METGEV  ++GF QF+ E +  +E+    ++IL+  ++I+ M +KF+</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+<Hit>
+  <Hit_num>3</Hit_num>
+  <Hit_id>gi|228861509|ref|YP_002854530.1|</Hit_id>
+  <Hit_def>alt.-2 hypothetical protein [Enterobacteria phage RB14] &gt;gi|227438525|gb|ACP30838.1| alt.-2 hypothetical protein [Enterobacteria phage RB14]</Hit_def>
+  <Hit_accession>YP_002854530</Hit_accession>
+  <Hit_len>685</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>197.593</Hsp_bit-score>
+      <Hsp_score>501</Hsp_score>
+      <Hsp_evalue>4.35388e-55</Hsp_evalue>
+      <Hsp_query-from>2</Hsp_query-from>
+      <Hsp_query-to>229</Hsp_query-to>
+      <Hsp_hit-from>474</Hsp_hit-from>
+      <Hsp_hit-to>684</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>108</Hsp_identity>
+      <Hsp_positive>152</Hsp_positive>
+      <Hsp_gaps>21</Hsp_gaps>
+      <Hsp_align-len>230</Hsp_align-len>
+      <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
+      <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGS-----------HSTYANEDAETSVGMVIKGAERVKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYFMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
+      <Hsp_midline>L  GT LYRGQ++   T  HN ENK+FYF+N+VSTSLKP IFGE G+ +MALDD   +++ E         + ED++ +G+             T  N   + ++G VI GAE V+VIVPG L+ +P EAEVILPRG LLKINK++T   K +  NK+++EG+IVPPSEQ++ESV  YDGD  METGEV  ++GF QF+ E +  +E+    ++IL+  ++I+ M +KF+</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>48094830</Statistics_db-num>
+      <Statistics_db-len>17186091396</Statistics_db-len>
+      <Statistics_hsp-len>143</Statistics_hsp-len>
+      <Statistics_eff-space>886533640716</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>
+