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comparison 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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2:b6a0e126dbee 3:7342f467507b
1 <?xml version="1.0"?>
2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
3 <BlastOutput>
4 <BlastOutput_program>blastp</BlastOutput_program>
5 <BlastOutput_version>BLASTP 2.2.28+</BlastOutput_version>
6 <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>
7 <BlastOutput_db>/usr/local/syncdb/community/nr/nr</BlastOutput_db>
8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
9 <BlastOutput_query-def>Merlin_1</BlastOutput_query-def>
10 <BlastOutput_query-len>229</BlastOutput_query-len>
11 <BlastOutput_param>
12 <Parameters>
13 <Parameters_matrix>BLOSUM62</Parameters_matrix>
14 <Parameters_expect>0.001</Parameters_expect>
15 <Parameters_gap-open>11</Parameters_gap-open>
16 <Parameters_gap-extend>1</Parameters_gap-extend>
17 <Parameters_filter>F</Parameters_filter>
18 </Parameters>
19 </BlastOutput_param>
20 <BlastOutput_iterations>
21 <Iteration>
22 <Iteration_iter-num>1</Iteration_iter-num>
23 <Iteration_query-ID>Query_1</Iteration_query-ID>
24 <Iteration_query-def>Merlin_1</Iteration_query-def>
25 <Iteration_query-len>229</Iteration_query-len>
26 <Iteration_hits>
27 <Hit>
28 <Hit_num>1</Hit_num>
29 <Hit_id>gi|422934611|ref|YP_007004572.1|</Hit_id>
30 <Hit_def>hypothetical protein [Enterobacteria phage ime09] &gt;gi|339791394|gb|AEK12451.1| hypothetical protein [Enterobacteria phage ime09]</Hit_def>
31 <Hit_accession>YP_007004572</Hit_accession>
32 <Hit_len>685</Hit_len>
33 <Hit_hsps>
34 <Hsp>
35 <Hsp_num>1</Hsp_num>
36 <Hsp_bit-score>197.593</Hsp_bit-score>
37 <Hsp_score>501</Hsp_score>
38 <Hsp_evalue>3.74548e-55</Hsp_evalue>
39 <Hsp_query-from>2</Hsp_query-from>
40 <Hsp_query-to>229</Hsp_query-to>
41 <Hsp_hit-from>474</Hsp_hit-from>
42 <Hsp_hit-to>684</Hsp_hit-to>
43 <Hsp_query-frame>0</Hsp_query-frame>
44 <Hsp_hit-frame>0</Hsp_hit-frame>
45 <Hsp_identity>106</Hsp_identity>
46 <Hsp_positive>154</Hsp_positive>
47 <Hsp_gaps>21</Hsp_gaps>
48 <Hsp_align-len>230</Hsp_align-len>
49 <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
50 <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGSHSAYANED-----------AETSVGMVIKGAERIKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYMMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
51 <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>
52 </Hsp>
53 </Hit_hsps>
54 </Hit>
55 <Hit>
56 <Hit_num>2</Hit_num>
57 <Hit_id>gi|330858714|ref|YP_004415089.1|</Hit_id>
58 <Hit_def>hypothetical protein Shfl2p198 [Shigella phage Shfl2] &gt;gi|327397648|gb|AEA73150.1| hypothetical protein Shfl2p198 [Shigella phage Shfl2]</Hit_def>
59 <Hit_accession>YP_004415089</Hit_accession>
60 <Hit_len>685</Hit_len>
61 <Hit_hsps>
62 <Hsp>
63 <Hsp_num>1</Hsp_num>
64 <Hsp_bit-score>197.593</Hsp_bit-score>
65 <Hsp_score>501</Hsp_score>
66 <Hsp_evalue>4.31042e-55</Hsp_evalue>
67 <Hsp_query-from>2</Hsp_query-from>
68 <Hsp_query-to>229</Hsp_query-to>
69 <Hsp_hit-from>474</Hsp_hit-from>
70 <Hsp_hit-to>684</Hsp_hit-to>
71 <Hsp_query-frame>0</Hsp_query-frame>
72 <Hsp_hit-frame>0</Hsp_hit-frame>
73 <Hsp_identity>106</Hsp_identity>
74 <Hsp_positive>154</Hsp_positive>
75 <Hsp_gaps>21</Hsp_gaps>
76 <Hsp_align-len>230</Hsp_align-len>
77 <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
78 <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGSHSAYANED-----------AETSVGMVIKGAERIKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYMMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
79 <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>
80 </Hsp>
81 </Hit_hsps>
82 </Hit>
83 <Hit>
84 <Hit_num>3</Hit_num>
85 <Hit_id>gi|228861509|ref|YP_002854530.1|</Hit_id>
86 <Hit_def>alt.-2 hypothetical protein [Enterobacteria phage RB14] &gt;gi|227438525|gb|ACP30838.1| alt.-2 hypothetical protein [Enterobacteria phage RB14]</Hit_def>
87 <Hit_accession>YP_002854530</Hit_accession>
88 <Hit_len>685</Hit_len>
89 <Hit_hsps>
90 <Hsp>
91 <Hsp_num>1</Hsp_num>
92 <Hsp_bit-score>197.593</Hsp_bit-score>
93 <Hsp_score>501</Hsp_score>
94 <Hsp_evalue>4.35388e-55</Hsp_evalue>
95 <Hsp_query-from>2</Hsp_query-from>
96 <Hsp_query-to>229</Hsp_query-to>
97 <Hsp_hit-from>474</Hsp_hit-from>
98 <Hsp_hit-to>684</Hsp_hit-to>
99 <Hsp_query-frame>0</Hsp_query-frame>
100 <Hsp_hit-frame>0</Hsp_hit-frame>
101 <Hsp_identity>108</Hsp_identity>
102 <Hsp_positive>152</Hsp_positive>
103 <Hsp_gaps>21</Hsp_gaps>
104 <Hsp_align-len>230</Hsp_align-len>
105 <Hsp_qseq>LDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIYTAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIVPGSLTEYPEEAEVILPRGTLLKINKITTQVDKRS--NKFMVEGSIVPPSEQIDESVEIYDGDLFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR</Hsp_qseq>
106 <Hsp_hseq>LPPGTTLYRGQEVTFKTLRHNIENKMFYFKNFVSTSLKPNIFGEHGKNYMALDDSGAVFSGEGEGS----VDAEDLMHMGS-----------HSTYANEDAETSVGMVIKGAERVKVIVPGHLSGFPSEAEVILPRGILLKINKVSTYFMKETAYNKYLIEGTIVPPSEQLEESV--YDGDHLMETGEVRPMAGFNQFLVEES--KEEENEVSQILASLVNINGMSKKFK</Hsp_hseq>
107 <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>
108 </Hsp>
109 </Hit_hsps>
110 </Hit>
111 </Iteration_hits>
112 <Iteration_stat>
113 <Statistics>
114 <Statistics_db-num>48094830</Statistics_db-num>
115 <Statistics_db-len>17186091396</Statistics_db-len>
116 <Statistics_hsp-len>143</Statistics_hsp-len>
117 <Statistics_eff-space>886533640716</Statistics_eff-space>
118 <Statistics_kappa>0.041</Statistics_kappa>
119 <Statistics_lambda>0.267</Statistics_lambda>
120 <Statistics_entropy>0.14</Statistics_entropy>
121 </Statistics>
122 </Iteration_stat>
123 </Iteration>
124 </BlastOutput_iterations>
125 </BlastOutput>
126