Mercurial > repos > devteam > ncbi_blast_plus
view test-data/blastn_arabidopsis.xml @ 33:d999e774072a draft
Fix for get_species_taxids
author | peterjc |
---|---|
date | Sun, 19 Nov 2023 22:57:39 +0000 |
parents | 4c4a0da938ff |
children |
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<?xml version="1.0"?> <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastn</BlastOutput_program> <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version> <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def> <BlastOutput_query-len>630</BlastOutput_query-len> <BlastOutput_param> <Parameters> <Parameters_expect>0.001</Parameters_expect> <Parameters_sc-match>1</Parameters_sc-match> <Parameters_sc-mismatch>-2</Parameters_sc-mismatch> <Parameters_gap-open>0</Parameters_gap-open> <Parameters_gap-extend>0</Parameters_gap-extend> <Parameters_filter>L;m;</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>chunk_of_plant</Iteration_query-def> <Iteration_query-len>630</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|2</Hit_id> <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def> <Hit_accession>2</Hit_accession> <Hit_len>23459830</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>1164.51</Hsp_bit-score> <Hsp_score>630</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>630</Hsp_query-to> <Hsp_hit-from>4341</Hsp_hit-from> <Hsp_hit-to>4970</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>630</Hsp_identity> <Hsp_positive>630</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>630</Hsp_align-len> <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq> <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq> <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>5</Statistics_db-num> <Statistics_db-len>119146348</Statistics_db-len> <Statistics_hsp-len>26</Statistics_hsp-len> <Statistics_eff-space>71964315672</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> </Statistics> </Iteration_stat> </Iteration> </BlastOutput_iterations> </BlastOutput>