Bio-FastParsers
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test/tblastx.xml view on Meta::CPAN
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>tblastx</BlastOutput_program>
<BlastOutput_version>TBLASTX 2.2.26+</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 program...
<BlastOutput_db>chlamy_mito</BlastOutput_db>
<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
<BlastOutput_query-def>gi|11465907|ref|NC_001872.1| Chlamydomonas eugametos mitochondrion, complete genome</BlastOutput_query-def>
<BlastOutput_query-len>22897</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>L;</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>gi|11465907|ref|NC_001872.1| Chlamydomonas eugametos mitochondrion, complete genome</Iteration_query-def>
<Iteration_query-len>22897</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|BL_ORD_ID|0</Hit_id>
<Hit_def>gi|11465907|ref|NC_001872.1| Chlamydomonas eugametos mitochondrion, complete genome</Hit_def>
<Hit_accession>0</Hit_accession>
<Hit_len>22897</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>3346.91</Hsp_bit-score>
<Hsp_score>7298</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>17974</Hsp_query-from>
<Hsp_query-to>22539</Hsp_query-to>
<Hsp_hit-from>17974</Hsp_hit-from>
<Hsp_hit-to>22539</Hsp_hit-to>
<Hsp_query-frame>-2</Hsp_query-frame>
<Hsp_hit-frame>-2</Hsp_hit-frame>
<Hsp_identity>1522</Hsp_identity>
<Hsp_positive>1522</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>1522</Hsp_align-len>
<Hsp_qseq>DAFTLGSSCVTNGPE*SYIYDWINNFAV*HDVINNAATYNNVCA*YVIAGEPPLYVE*AKFIIASLE*KPDVSGNPTKHIHPIINVKKQNIELWVTDNPPYLAICWFPLVDIIITPXXXXXXXXXXACVIK*VIDASAPYEPNPTLTIMYPNCEHVLNAITRFKSA*KKPNIPAINAVKLPTIITKSDPTINALKRTIK*TPAVTKVAAWIKADTGVGFFINRPFP...
<Hsp_hseq>DAFTLGSSCVTNGPE*SYIYDWINNFAV*HDVINNAATYNNVCA*YVIAGEPPLYVE*AKFIIASLE*KPDVSGNPTKHIHPIINVKKQNIELWVTDNPPYLAICWFPLVDIIITPAAKNNAALKLACVIK*VIDASAPYEPNPTLTIMYPNCEHVLNAITRFKSA*KKPNIPAINAVKLPTIITKSDPTINALKRTIK*TPAVTKVAAWIKADTGVGFFINRPFP...
<Hsp_midline>DAFTLGSSCVTNGPE*SYIYDWINNFAV*HDVINNAATYNNVCA*YVIAGEPPLYVE*AKFIIASLE*KPDVSGNPTKHIHPIINVKKQNIELWVTDNPPYLAICWFPLVDIIITPAAKNNAALKLACVIK*VIDASAPYEPNPTLTIMYPNCEHVLNAITRFKSA*KKPNIPAINAVKLPTIITKSDPTINALKRTIK*TPAVTKVAAWIKADTGVGFFINR...
</Hsp>
<Hsp>
<Hsp_num>2</Hsp_num>
<Hsp_bit-score>2966.59</Hsp_bit-score>
<Hsp_score>6468</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>12910</Hsp_query-from>
<Hsp_query-to>16836</Hsp_query-to>
<Hsp_hit-from>12910</Hsp_hit-from>
<Hsp_hit-to>16836</Hsp_hit-to>
<Hsp_query-frame>-2</Hsp_query-frame>
<Hsp_hit-frame>-2</Hsp_hit-frame>
<Hsp_identity>1309</Hsp_identity>
<Hsp_positive>1309</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>1309</Hsp_align-len>
<Hsp_qseq>LHTSHNLTFS*CKKGDT*QYRYCNR*N**YNHY*FSKASY*MIL*DRTLA*RQSLN*ANKDRTCDLGTKTQCLATWL*LKRSRKNKI*TCNHRIWNPIL*PLSYPSMYF*LN**LRMTGNCINT*LAGVEWSIHSKVVALRG*VLDLVLISGIKFIGPANIKIDKNDINATKLAIEFQP*KQSA*SNILRGMPPRPIICIGKNVKLTPINKVQNCT*PRLSI*VSP...
<Hsp_hseq>LHTSHNLTFS*CKKGDT*QYRYCNR*N**YNHY*FSKASY*MIL*DRTLA*RQSLN*ANKDRTCDLGTKTQCLATWL*LKRSRKNKI*TCNHRIWNPIL*PLSYPSMYF*LN**LRMTGNCINT*LAGVEWSIHSKVVALRG*VLDLVLISGIKFIGPANIKIDKNDINATKLAIEFQP*KQSA*SNILRGMPPRPIICIGKNVKLTPINKVQNCT*PRLSI*VSP...
<Hsp_midline>LHTSHNLTFS*CKKGDT*QYRYCNR*N**YNHY*FSKASY*MIL*DRTLA*RQSLN*ANKDRTCDLGTKTQCLATWL*LKRSRKNKI*TCNHRIWNPIL*PLSYPSMYF*LN**LRMTGNCINT*LAGVEWSIHSKVVALRG*VLDLVLISGIKFIGPANIKIDKNDINATKLAIEFQP*KQSA*SNILRGMPPRPIICIGKNVKLTPINKVQNCT*PRLSI*...
</Hsp>
<Hsp>
<Hsp_num>3</Hsp_num>
<Hsp_bit-score>1897.13</Hsp_bit-score>
<Hsp_score>4134</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>19148</Hsp_query-from>
<Hsp_query-to>21544</Hsp_query-to>
<Hsp_hit-from>19148</Hsp_hit-from>
<Hsp_hit-to>21544</Hsp_hit-to>
test/tblastx.xml view on Meta::CPAN
<Hsp_positive>25</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>37</Hsp_align-len>
<Hsp_qseq>SDIKR*GLMXXXXXXXXEVKVPNCFFLKKK*TLALSS</Hsp_qseq>
<Hsp_hseq>SDNRR*GQLSRGEQSRGEAKVPNNYYIQIALALLKSS</Hsp_hseq>
<Hsp_midline>SD +R*G +S+G++S E KVPN ++++ L SS</Hsp_midline>
</Hsp>
<Hsp>
<Hsp_num>162</Hsp_num>
<Hsp_bit-score>24.436</Hsp_bit-score>
<Hsp_score>47</Hsp_score>
<Hsp_evalue>8.57396</Hsp_evalue>
<Hsp_query-from>20599</Hsp_query-from>
<Hsp_query-to>20634</Hsp_query-to>
<Hsp_hit-from>4491</Hsp_hit-from>
<Hsp_hit-to>4526</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>9</Hsp_identity>
<Hsp_positive>11</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>12</Hsp_align-len>
<Hsp_qseq>RCLFLPINWLLQ</Hsp_qseq>
<Hsp_hseq>RCLFLPIDRLLE</Hsp_hseq>
<Hsp_midline>RCLFLPI+ LL+</Hsp_midline>
</Hsp>
<Hsp>
<Hsp_num>163</Hsp_num>
<Hsp_bit-score>24.436</Hsp_bit-score>
<Hsp_score>47</Hsp_score>
<Hsp_evalue>8.57396</Hsp_evalue>
<Hsp_query-from>7985</Hsp_query-from>
<Hsp_query-to>8083</Hsp_query-to>
<Hsp_hit-from>1474</Hsp_hit-from>
<Hsp_hit-to>1572</Hsp_hit-to>
<Hsp_query-frame>2</Hsp_query-frame>
<Hsp_hit-frame>-3</Hsp_hit-frame>
<Hsp_identity>17</Hsp_identity>
<Hsp_positive>18</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>33</Hsp_align-len>
<Hsp_qseq>*LVKL*QVYY*RCIM*VMLIMHLQVYNI*W*MY</Hsp_qseq>
<Hsp_hseq>*LVKCLLVFY*PCTM*VT*TTLLLAYNT**LMY</Hsp_hseq>
<Hsp_midline>*LVK V+Y* C M*V L YN * MY</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>2</Statistics_db-num>
<Statistics_db-len>38655</Statistics_db-len>
<Statistics_hsp-len>37</Statistics_hsp-len>
<Statistics_eff-space>97299545</Statistics_eff-space>
<Statistics_kappa>0.133956144488482</Statistics_kappa>
<Statistics_lambda>0.317605957635731</Statistics_lambda>
<Statistics_entropy>0.401214524497119</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
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