Bio-FastParsers
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test/tblastn.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>tblastn</BlastOutput_program>
<BlastOutput_version>TBLASTN 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>nt</BlastOutput_db>
<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
<BlastOutput_query-def>gi|2105139|gb|AAC47544.1| hemoglobin [Daphnia magna]</BlastOutput_query-def>
<BlastOutput_query-len>348</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|2105139|gb|AAC47544.1| hemoglobin [Daphnia magna]</Iteration_query-def>
<Iteration_query-len>348</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|2105138|gb|U67067.1|DMU67067</Hit_id>
<Hit_def>Daphnia magna hemoglobin (Dhb1) mRNA, complete cds</Hit_def>
<Hit_accession>U67067</Hit_accession>
<Hit_len>1261</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>681.019</Hsp_bit-score>
<Hsp_score>1756</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>348</Hsp_query-to>
<Hsp_hit-from>75</Hsp_hit-from>
<Hsp_hit-to>1118</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>3</Hsp_hit-frame>
<Hsp_identity>348</Hsp_identity>
<Hsp_positive>348</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>348</Hsp_align-len>
<Hsp_qseq>MASFKIALLLGVIAFVNACSQAPGXXXXXXXXXXXXXSADDGSEAGLLSAHERSLIRKTWDQAKKDGDVAPQVLFRFVKAHPEYQKMFSKFANVPQSELLSNGNFLAQAYTILAGLNVVIQSLFSQELMANQLNALGGAHQPRGATPVMFEQFGGILEEVLAEELGSGFTAEARQAWKNGLAALVAGIAKNLKKAEDLADPQTKLTPHQIRDVQRSWENIRNDRNA...
<Hsp_hseq>MASFKIALLLGVIAFVNACSQAPGTTTTTVTTTVTTVSADDGSEAGLLSAHERSLIRKTWDQAKKDGDVAPQVLFRFVKAHPEYQKMFSKFANVPQSELLSNGNFLAQAYTILAGLNVVIQSLFSQELMANQLNALGGAHQPRGATPVMFEQFGGILEEVLAEELGSGFTAEARQAWKNGLAALVAGIAKNLKKAEDLADPQTKLTPHQIRDVQRSWENIRNDRNA...
<Hsp_midline>MASFKIALLLGVIAFVNACSQAPGTTTTTVTTTVTTVSADDGSEAGLLSAHERSLIRKTWDQAKKDGDVAPQVLFRFVKAHPEYQKMFSKFANVPQSELLSNGNFLAQAYTILAGLNVVIQSLFSQELMANQLNALGGAHQPRGATPVMFEQFGGILEEVLAEELGSGFTAEARQAWKNGLAALVAGIAKNLKKAEDLADPQTKLTPHQIRDVQRSWENIRND...
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
<Hit_num>2</Hit_num>
<Hit_id>gi|4589711|dbj|AB021137.1|</Hit_id>
<Hit_def>Daphnia magna dhb3 mRNA for hemoglobin, complete cds</Hit_def>
<Hit_accession>AB021137</Hit_accession>
<Hit_len>1180</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>630.558</Hsp_bit-score>
<Hsp_score>1625</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>347</Hsp_query-to>
<Hsp_hit-from>34</Hsp_hit-from>
<Hsp_hit-to>1074</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>318</Hsp_identity>
<Hsp_positive>335</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>347</Hsp_align-len>
<Hsp_qseq>MASFKIALLLGVIAFVNACSQAPGXXXXXXXXXXXXXSADDGSEAGLLSAHERSLIRKTWDQAKKDGDVAPQVLFRFVKAHPEYQKMFSKFANVPQSELLSNGNFLAQAYTILAGLNVVIQSLFSQELMANQLNALGGAHQPRGATPVMFEQFGGILEEVLAEELGSGFTAEARQAWKNGLAALVAGIAKNLKKAEDLADPQTKLTPHQIRDVQRSWENIRNDRNA...
<Hsp_hseq>MASFKIALLFGVVAFVSAYSQAPGTTTTTVTTTVTTVSADDGSEAGILSAHERSLIRKTWEQARKDGDVAPQILFRFVKAHPEYQKMFSKFANVPQAELLTNGNFLAQAYTILAGLNVVVQSLSSQELMANQLNALGGAHKPRGATPVMFEQFGGILEEVLAEELGSSFTAEARQAWKNGLTALISGISKNLKKAEDLADPQTKLTPHQIQDVQRSWENIRNGRNA...
<Hsp_midline>MASFKIALL GV+AFV+A SQAPGTTTTTVTTTVTTVSADDGSEAG+LSAHERSLIRKTW+QA+KDGDVAPQ+LFRFVKAHPEYQKMFSKFANVPQ+ELL+NGNFLAQAYTILAGLNVV+QSL SQELMANQLNALGGAH+PRGATPVMFEQFGGILEEVLAEELGS FTAEARQAWKNGL AL++GI+KNLKKAEDLADPQTKLTPHQI+DVQRSWENIRN ...
</Hsp>
test/tblastn.xml view on Meta::CPAN
<Hsp_positive>83</Hsp_positive>
<Hsp_gaps>6</Hsp_gaps>
<Hsp_align-len>97</Hsp_align-len>
<Hsp_qseq>KLFKETPRIQKFFAKFANVAVDSLAGNAEYEKQIALVADRLDTMISAMDDKLQLLGNINYMRYTHTERGIPRAPWEDFSRLLLDVLGSKGVSTDDLD</Hsp_qseq>
<Hsp_hseq>RLFKETPRIQKFFAKFGNVAVDSLAGNADYEKQVALVADRLDTIISAMDDKLQLLGNINYMRYTHTERGIPRGPWEVHQRRL------KNISQDEID</Hsp_hseq>
<Hsp_midline>+LFKETPRIQKFFAKF NVAVDSLAGNA+YEKQ+ALVADRLDT+ISAMDDKLQLLGNINYMRYTHTERGIPR PWE R L K +S D++D</Hsp_midline>
</Hsp>
<Hsp>
<Hsp_num>3</Hsp_num>
<Hsp_bit-score>85.8853</Hsp_bit-score>
<Hsp_score>211</Hsp_score>
<Hsp_evalue>1.04128e-126</Hsp_evalue>
<Hsp_query-from>189</Hsp_query-from>
<Hsp_query-to>234</Hsp_query-to>
<Hsp_hit-from>673</Hsp_hit-from>
<Hsp_hit-to>810</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>40</Hsp_identity>
<Hsp_positive>43</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>46</Hsp_align-len>
<Hsp_qseq>AKNLKKAEDLADPQTKLTPHQIRDVQRSWENIRNDRNALVSSIFVK</Hsp_qseq>
<Hsp_hseq>AINFRKSEDLADPQTKLTPHQIQDVQRSWENIRNGRNALVSSIFVK</Hsp_hseq>
<Hsp_midline>A N +K+EDLADPQTKLTPHQI+DVQRSWENIRN RNALVSSIFVK</Hsp_midline>
</Hsp>
<Hsp>
<Hsp_num>4</Hsp_num>
<Hsp_bit-score>63.5438</Hsp_bit-score>
<Hsp_score>153</Hsp_score>
<Hsp_evalue>1.04128e-126</Hsp_evalue>
<Hsp_query-from>47</Hsp_query-from>
<Hsp_query-to>76</Hsp_query-to>
<Hsp_hit-from>1</Hsp_hit-from>
<Hsp_hit-to>90</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>28</Hsp_identity>
<Hsp_positive>30</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>30</Hsp_align-len>
<Hsp_qseq>LLSAHERSLIRKTWDQAKKDGDVAPQVLFR</Hsp_qseq>
<Hsp_hseq>ILSSHERSLIRKTWDQAKKDGDVAPQVLFR</Hsp_hseq>
<Hsp_midline>+LS+HERSLIRKTWDQAKKDGDVAPQVLFR</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>16789277</Statistics_db-num>
<Statistics_db-len>43111105184</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>2422090766106</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
( run in 0.832 second using v1.01-cache-2.11-cpan-71847e10f99 )