Mercurial > repos > jankanis > blast2html
view test-data/blast xml example4.xml @ 100:be7c94e29cd8
add --db-config-dir switch to wrapper; update version number
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Tue, 01 Jul 2014 16:23:29 +0200 |
| parents | 0ef071bba164 |
| 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 2.2.29+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db>/opt/galaxy/blastdbs/EUginius_plasmid_insert</BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def> <BlastOutput_query-len>20</BlastOutput_query-len> <BlastOutput_param> <Parameters> <Parameters_expect>0.001</Parameters_expect> <Parameters_sc-match>1</Parameters_sc-match> <Parameters_sc-mismatch>-3</Parameters_sc-mismatch> <Parameters_gap-open>5</Parameters_gap-open> <Parameters_gap-extend>2</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def> <Iteration_query-len>20</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|5</Hit_id> <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def> <Hit_accession>5</Hit_accession> <Hit_len>2457</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>40.14</Hsp_bit-score> <Hsp_score>20</Hsp_score> <Hsp_evalue>1.51296e-07</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>20</Hsp_query-to> <Hsp_hit-from>2119</Hsp_hit-from> <Hsp_hit-to>2138</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>20</Hsp_identity> <Hsp_positive>20</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>20</Hsp_align-len> <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq> <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq> <Hsp_midline>||||||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> <Hit> <Hit_num>2</Hit_num> <Hit_id>gnl|BL_ORD_ID|2</Hit_id> <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def> <Hit_accession>2</Hit_accession> <Hit_len>323</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>40.14</Hsp_bit-score> <Hsp_score>20</Hsp_score> <Hsp_evalue>1.51296e-07</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>20</Hsp_query-to> <Hsp_hit-from>200</Hsp_hit-from> <Hsp_hit-to>219</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>20</Hsp_identity> <Hsp_positive>20</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>20</Hsp_align-len> <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq> <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq> <Hsp_midline>||||||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>8</Statistics_hsp-len> <Statistics_eff-space>183300</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> </Iteration> <Iteration> <Iteration_iter-num>2</Iteration_iter-num> <Iteration_query-ID>Query_2</Iteration_query-ID> <Iteration_query-def>Reverse_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def> <Iteration_query-len>20</Iteration_query-len> <Iteration_hits> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>8</Statistics_hsp-len> <Statistics_eff-space>183300</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> <Iteration_message>No hits found</Iteration_message> </Iteration> <Iteration> <Iteration_iter-num>3</Iteration_iter-num> <Iteration_query-ID>Query_3</Iteration_query-ID> <Iteration_query-def>Probe|NOST-Spec_(Genetic_ID)</Iteration_query-def> <Iteration_query-len>20</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|5</Hit_id> <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def> <Hit_accession>5</Hit_accession> <Hit_len>2457</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>40.14</Hsp_bit-score> <Hsp_score>20</Hsp_score> <Hsp_evalue>1.51296e-07</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>20</Hsp_query-to> <Hsp_hit-from>2143</Hsp_hit-from> <Hsp_hit-to>2162</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>20</Hsp_identity> <Hsp_positive>20</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>20</Hsp_align-len> <Hsp_qseq>CGCGCGCGGTGTCATCTATG</Hsp_qseq> <Hsp_hseq>CGCGCGCGGTGTCATCTATG</Hsp_hseq> <Hsp_midline>||||||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> <Hit> <Hit_num>2</Hit_num> <Hit_id>gnl|BL_ORD_ID|2</Hit_id> <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def> <Hit_accession>2</Hit_accession> <Hit_len>323</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>40.14</Hsp_bit-score> <Hsp_score>20</Hsp_score> <Hsp_evalue>1.51296e-07</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>20</Hsp_query-to> <Hsp_hit-from>224</Hsp_hit-from> <Hsp_hit-to>243</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>20</Hsp_identity> <Hsp_positive>20</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>20</Hsp_align-len> <Hsp_qseq>CGCGCGCGGTGTCATCTATG</Hsp_qseq> <Hsp_hseq>CGCGCGCGGTGTCATCTATG</Hsp_hseq> <Hsp_midline>||||||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> <Hit> <Hit_num>3</Hit_num> <Hit_id>gnl|BL_ORD_ID|1</Hit_id> <Hit_def>AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000</Hit_def> <Hit_accession>1</Hit_accession> <Hit_len>1045</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>34.1929</Hsp_bit-score> <Hsp_score>17</Hsp_score> <Hsp_evalue>9.33411e-06</Hsp_evalue> <Hsp_query-from>4</Hsp_query-from> <Hsp_query-to>20</Hsp_query-to> <Hsp_hit-from>2</Hsp_hit-from> <Hsp_hit-to>18</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>17</Hsp_identity> <Hsp_positive>17</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>17</Hsp_align-len> <Hsp_qseq>GCGCGGTGTCATCTATG</Hsp_qseq> <Hsp_hseq>GCGCGGTGTCATCTATG</Hsp_hseq> <Hsp_midline>|||||||||||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>8</Statistics_hsp-len> <Statistics_eff-space>183300</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> </Iteration> <Iteration> <Iteration_iter-num>4</Iteration_iter-num> <Iteration_query-ID>Query_4</Iteration_query-ID> <Iteration_query-def>Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def> <Iteration_query-len>24</Iteration_query-len> <Iteration_hits> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>9</Statistics_hsp-len> <Statistics_eff-space>229005</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> <Iteration_message>No hits found</Iteration_message> </Iteration> <Iteration> <Iteration_iter-num>5</Iteration_iter-num> <Iteration_query-ID>Query_5</Iteration_query-ID> <Iteration_query-def>Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def> <Iteration_query-len>20</Iteration_query-len> <Iteration_hits> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>8</Statistics_hsp-len> <Statistics_eff-space>183300</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> <Iteration_message>No hits found</Iteration_message> </Iteration> <Iteration> <Iteration_iter-num>6</Iteration_iter-num> <Iteration_query-ID>Query_6</Iteration_query-ID> <Iteration_query-def>Probe|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def> <Iteration_query-len>25</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|7</Hit_id> <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def> <Hit_accession>7</Hit_accession> <Hit_len>4983</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>36.1753</Hsp_bit-score> <Hsp_score>18</Hsp_score> <Hsp_evalue>3.14801e-06</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>22</Hsp_query-to> <Hsp_hit-from>2344</Hsp_hit-from> <Hsp_hit-to>2365</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>21</Hsp_identity> <Hsp_positive>21</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>22</Hsp_align-len> <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq> <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq> <Hsp_midline>|||||||||||||| |||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> <Hit> <Hit_num>2</Hit_num> <Hit_id>gnl|BL_ORD_ID|6</Hit_id> <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def> <Hit_accession>6</Hit_accession> <Hit_len>4180</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>36.1753</Hsp_bit-score> <Hsp_score>18</Hsp_score> <Hsp_evalue>3.14801e-06</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>22</Hsp_query-to> <Hsp_hit-from>1541</Hsp_hit-from> <Hsp_hit-to>1562</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>21</Hsp_identity> <Hsp_positive>21</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>22</Hsp_align-len> <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq> <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq> <Hsp_midline>|||||||||||||| |||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>9</Statistics_hsp-len> <Statistics_eff-space>244272</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> </Iteration> <Iteration> <Iteration_iter-num>7</Iteration_iter-num> <Iteration_query-ID>Query_7</Iteration_query-ID> <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def> <Iteration_query-len>74</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|7</Hit_id> <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def> <Hit_accession>7</Hit_accession> <Hit_len>4983</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>67.8929</Hsp_bit-score> <Hsp_score>34</Hsp_score> <Hsp_evalue>3.56369e-15</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>74</Hsp_query-to> <Hsp_hit-from>2319</Hsp_hit-from> <Hsp_hit-to>2392</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>1</Hsp_hit-frame> <Hsp_identity>64</Hsp_identity> <Hsp_positive>64</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>74</Hsp_align-len> <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq> <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq> <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> <Hit> <Hit_num>2</Hit_num> <Hit_id>gnl|BL_ORD_ID|6</Hit_id> <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def> <Hit_accession>6</Hit_accession> <Hit_len>4180</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>67.8929</Hsp_bit-score> <Hsp_score>34</Hsp_score> <Hsp_evalue>3.56369e-15</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>74</Hsp_query-to> <Hsp_hit-from>1589</Hsp_hit-from> <Hsp_hit-to>1516</Hsp_hit-to> <Hsp_query-frame>1</Hsp_query-frame> <Hsp_hit-frame>-1</Hsp_hit-frame> <Hsp_identity>64</Hsp_identity> <Hsp_positive>64</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>74</Hsp_align-len> <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq> <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq> <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline> </Hsp> </Hit_hsps> </Hit> </Iteration_hits> <Iteration_stat> <Statistics> <Statistics_db-num>8</Statistics_db-num> <Statistics_db-len>15339</Statistics_db-len> <Statistics_hsp-len>10</Statistics_hsp-len> <Statistics_eff-space>976576</Statistics_eff-space> <Statistics_kappa>0.710602795216363</Statistics_kappa> <Statistics_lambda>1.37406312246009</Statistics_lambda> <Statistics_entropy>1.30724660390929</Statistics_entropy> </Statistics> </Iteration_stat> </Iteration> </BlastOutput_iterations> </BlastOutput>