Mercurial > repos > devteam > ncbi_blast_plus

annotate test-data/blastn_arabidopsis.xml @ 6:856b73016ba1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.1.05 - Update citation information now GigaScience paper is out
author peterjc
date Fri, 04 Sep 2015 09:45:13 -0400
parents 432ea9614cc9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
1 <?xml version="1.0"?>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
3 <BlastOutput>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
4 <BlastOutput_program>blastn</BlastOutput_program>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
5 <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
6 <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
7 <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
9 <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
10 <BlastOutput_query-len>630</BlastOutput_query-len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
11 <BlastOutput_param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
12 <Parameters>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
13 <Parameters_expect>0.001</Parameters_expect>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
14 <Parameters_sc-match>1</Parameters_sc-match>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
15 <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
16 <Parameters_gap-open>0</Parameters_gap-open>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
17 <Parameters_gap-extend>0</Parameters_gap-extend>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
18 <Parameters_filter>L;m;</Parameters_filter>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
19 </Parameters>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
20 </BlastOutput_param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
21 <BlastOutput_iterations>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
22 <Iteration>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
23 <Iteration_iter-num>1</Iteration_iter-num>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
24 <Iteration_query-ID>Query_1</Iteration_query-ID>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
25 <Iteration_query-def>chunk_of_plant</Iteration_query-def>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
26 <Iteration_query-len>630</Iteration_query-len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
27 <Iteration_hits>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
28 <Hit>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
29 <Hit_num>1</Hit_num>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
30 <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
31 <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
32 <Hit_accession>2</Hit_accession>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
33 <Hit_len>23459830</Hit_len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
34 <Hit_hsps>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
35 <Hsp>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
36 <Hsp_num>1</Hsp_num>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
37 <Hsp_bit-score>1164.51</Hsp_bit-score>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
38 <Hsp_score>630</Hsp_score>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
39 <Hsp_evalue>0</Hsp_evalue>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
40 <Hsp_query-from>1</Hsp_query-from>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
41 <Hsp_query-to>630</Hsp_query-to>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
42 <Hsp_hit-from>4341</Hsp_hit-from>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
43 <Hsp_hit-to>4970</Hsp_hit-to>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
44 <Hsp_query-frame>1</Hsp_query-frame>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
45 <Hsp_hit-frame>1</Hsp_hit-frame>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
46 <Hsp_identity>630</Hsp_identity>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
47 <Hsp_positive>630</Hsp_positive>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
48 <Hsp_gaps>0</Hsp_gaps>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
49 <Hsp_align-len>630</Hsp_align-len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
50 <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
51 <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
52 <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
53 </Hsp>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
54 </Hit_hsps>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
55 </Hit>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
56 </Iteration_hits>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
57 <Iteration_stat>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
58 <Statistics>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
59 <Statistics_db-num>5</Statistics_db-num>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
60 <Statistics_db-len>119146348</Statistics_db-len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
61 <Statistics_hsp-len>26</Statistics_hsp-len>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
62 <Statistics_eff-space>71964315672</Statistics_eff-space>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
63 <Statistics_kappa>0.46</Statistics_kappa>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
64 <Statistics_lambda>1.28</Statistics_lambda>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
65 <Statistics_entropy>0.85</Statistics_entropy>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
66 </Statistics>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
67 </Iteration_stat>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
68 </Iteration>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
69 </BlastOutput_iterations>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
70 </BlastOutput>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
71