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view test-data/blast xml example4.xml @ 33:3bb5da68305e

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add test update script, add url to github page
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 15 May 2014 17:29:44 +0200
parents ce8f29efc0a1
children 0ef071bba164
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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&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>/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&apos;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>1516</Hsp_hit-from>
      <Hsp_hit-to>1589</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>