Bio-SearchIO-blastxml
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t/data/psiblast.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>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.2.16 [Mar-25-2007]</BlastOutput_version>
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~p...
<BlastOutput_db>AL591824.faa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|1373160|gb|AAB57770.1| PyrR</BlastOutput_query-def>
<BlastOutput_query-len>173</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_include>0.002</Parameters_include>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|16411294|emb|CAC99918.1|</Hit_id>
<Hit_def>pyrR [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAC99918</Hit_accession>
<Hit_len>183</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>209.92</Hsp_bit-score>
<Hsp_score>533</Hsp_score>
<Hsp_evalue>4.5377e-56</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>171</Hsp_query-to>
<Hsp_hit-from>1</Hsp_hit-from>
<Hsp_hit-to>172</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>117</Hsp_identity>
<Hsp_positive>140</Hsp_positive>
<Hsp_gaps>1</Hsp_gaps>
<Hsp_align-len>172</Hsp_align-len>
<Hsp_qseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLS-KKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQ</Hsp_qseq>
<Hsp_hseq>MQKQVVVMDEAAIKRALTRVSYEIIERNKGTKNLALVGIKTRGIYLAERLHKRILEIEGIDVPVGDIDITLYRDDLSFKDDKTREPAVHGTNIPFDINGKKVVLVDDVLYTGRTVRAAMDALMDVGRPAQIHLAVLADRGHRELPIRADYVGKNIPTSGNERVEVRLTDVDH</Hsp_hseq>
<Hsp_midline>M ++ V++DE AI+RALTR+++E+IERNKG N LVGIKTRGIYLA+RL +RI +IEG V VG+IDITLYRDDLS K EP V G +IP DI +KV+LVDDVLYTGRTVRA MDAL+DVGRP+ I LAVL DRGHRELPIRADY+GKNIPTS +E+V V+L +VD </Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
<Hit_num>2</Hit_num>
<Hit_id>gi|16409584|emb|CAD00746.1|</Hit_id>
<Hit_def>fusion protein, N-terminal part similar to B. subtilis YacA protein, C-terminal part similar to hypoxanthine-guanine phosphoribosyltransferase [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAD00746</Hit_accession>
<Hit_len>648</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>37.7354</Hsp_bit-score>
<Hsp_score>86</Hsp_score>
<Hsp_evalue>0.000286309</Hsp_evalue>
<Hsp_query-from>4</Hsp_query-from>
<Hsp_query-to>155</Hsp_query-to>
<Hsp_hit-from>475</Hsp_hit-from>
<Hsp_hit-to>617</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>32</Hsp_identity>
<Hsp_positive>78</Hsp_positive>
<Hsp_gaps>11</Hsp_gaps>
<Hsp_align-len>153</Hsp_align-len>
<Hsp_qseq>KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDR-GHRELPIRADYIGKNIP</Hsp_qseq>
<Hsp_hseq>QKVLISEDELQEKIRELGRELTTEYEG-RNPLVVGVLKGATPFMTDLLKRVDTY----LEMDFMDVSSYGN--GTVSSGEVKIIK--DLNASVEGRDVLVIEDIIDSGRTLSYLVD-LIKYRKAKSVKLVTLLDKPAGRNVEIEADYVGFVVP</Hsp_hseq>
<Hsp_midline>+ V++ E ++ + + E+ +G N ++VG+ L +R++ + + +D++ Y + +S + ++K D+ + + V++++D++ +GRT+ +D L+ + S++L L+D+ R + I ADY+G +P</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
t/data/psiblast.xml view on Meta::CPAN
<Hsp_score>50</Hsp_score>
<Hsp_evalue>4.74252</Hsp_evalue>
<Hsp_query-from>36</Hsp_query-from>
<Hsp_query-to>108</Hsp_query-to>
<Hsp_hit-from>190</Hsp_hit-from>
<Hsp_hit-to>251</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>15</Hsp_identity>
<Hsp_positive>29</Hsp_positive>
<Hsp_gaps>19</Hsp_gaps>
<Hsp_align-len>77</Hsp_align-len>
<Hsp_qseq>LVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGAD----IPVDITDQKVILVDDVL</Hsp_qseq>
<Hsp_hseq>LFGEPVKATYFATKLPTGVDGLGPIILEYPTFNIT---------------IIQGKNSQSFLPSEIYGQKGTLIVDPL</Hsp_hseq>
<Hsp_midline>L G + Y A +L ++ + + +IT +++G + +P +I QK L+ D L</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
<Hit_num>16</Hit_num>
<Hit_id>gi|16411460|emb|CAD00085.1|</Hit_id>
<Hit_def>lmo2007 [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAD00085</Hit_accession>
<Hit_len>485</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>22.9011</Hsp_bit-score>
<Hsp_score>48</Hsp_score>
<Hsp_evalue>7.56717</Hsp_evalue>
<Hsp_query-from>47</Hsp_query-from>
<Hsp_query-to>114</Hsp_query-to>
<Hsp_hit-from>51</Hsp_hit-from>
<Hsp_hit-to>137</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>19</Hsp_identity>
<Hsp_positive>35</Hsp_positive>
<Hsp_gaps>19</Hsp_gaps>
<Hsp_align-len>87</Hsp_align-len>
<Hsp_qseq>AKRLAERIEQIEGNPVTVGEIDITLYRDDLSKK-TSNDEPLV-------------KGADIP----VDITDQKVIL-VDDVLYTGRTV</Hsp_qseq>
<Hsp_hseq>MKEVNKYTEEKIGVKVEMTQIDWGDYGKRMQTVINSGENFDIAYSAAGEFVSYSQKGAFLPLNKYLDKEGKKMKAELNDVLWEGATI</Hsp_hseq>
<Hsp_midline> K + + E+ G V + +ID Y + S + + KGA +P +D +K+ ++DVL+ G T+</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>2846</Statistics_db-num>
<Statistics_db-len>870878</Statistics_db-len>
<Statistics_hsp-len>75</Statistics_hsp-len>
<Statistics_eff-space>6.44279e+07</Statistics_eff-space>
<Statistics_kappa>0.0475563</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>CONVERGED</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.2.16 [Mar-25-2007]</BlastOutput_version>
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~p...
<BlastOutput_db>AL591824.faa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|154350371|gb|ABS72450.1| DnaN [Bacillus amyloliquefaciens FZB42]</BlastOutput_query-def>
<BlastOutput_query-len>378</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_include>0.002</Parameters_include>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|16409361|emb|CAC98217.1|</Hit_id>
<Hit_def>DNA polymerase III, beta chain [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAC98217</Hit_accession>
<Hit_len>381</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>420.239</Hsp_bit-score>
<Hsp_score>1079</Hsp_score>
<Hsp_evalue>5.57178e-119</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>378</Hsp_query-to>
<Hsp_hit-from>1</Hsp_hit-from>
<Hsp_hit-to>381</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>221</Hsp_identity>
<Hsp_positive>293</Hsp_positive>
<Hsp_gaps>3</Hsp_gaps>
<Hsp_align-len>381</Hsp_align-len>
<Hsp_qseq>MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDEGVSFTGSDSDISIESFIPKEDDDKEIVTIDQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSASETRPILTGVNWKVENGELLCTATDSHRLALRKAKLDIPEDSSYNVVIPGKSLTELSKILDDNQELVDIVI...
<Hsp_hseq>MKFVIERDRLVQAVNEVTRAISARTTIPILTGIKIVVNDEGVTLTGSDSDISIEAFIPLIENDEVIVEVESFGGIVLQSKYFGDIVRRLPEENVEIEVTSNYQTNISSGQASFTLNGLDPMEYPKLPEVTDGKTIKIPINVLKNIVRQTVFAVSAIEVRPVLTGVNWIIKENKLSAVATDSHRLALREIPLETDIDEEYNIVIPGKSLSELNKLLDDASESIEMTL...
<Hsp_midline>MKF I++DRLV++V +V +A+S+RTTIPILTGIKIV +DEGV+ TGSDSDISIE+FIP ++D+ IV ++ G IVLQ+++F +IV++LP VEIEV + Y T I SG+A F LNGLD EYP LP++ + I+IP ++LKN++RQTVFAVSA E RP+LTGVNW ++ +L ATDSHRLALR+ L+ D YN+VIPGKSL+EL+K+LDD E ++...
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
<Hit_num>2</Hit_num>
<Hit_id>gi|16409959|emb|CAC98662.1|</Hit_id>
<Hit_def>lmo0583 [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAC98662</Hit_accession>
<Hit_len>776</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>32.7278</Hsp_bit-score>
<Hsp_score>73</Hsp_score>
<Hsp_evalue>0.0242028</Hsp_evalue>
<Hsp_query-from>63</Hsp_query-from>
<Hsp_query-to>181</Hsp_query-to>
<Hsp_hit-from>304</Hsp_hit-from>
<Hsp_hit-to>432</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>31</Hsp_identity>
<Hsp_positive>52</Hsp_positive>
<Hsp_gaps>10</Hsp_gaps>
<Hsp_align-len>129</Hsp_align-len>
<Hsp_qseq>DKEIVTIDQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTI--------IRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNL--IRQTVFAVSASETRPILTGVNWKVENGELLCTATDS</Hsp_qseq>
<Hsp_hseq>DDEVLIIDPHTGRALPGRRFNDGLHQAIEAKEGVEVKEESRTLATITIQNYFRMYKKISGMTGTAKTEEEEFRQIYNMDVVVIPTNLRVNREDMQDDIFYTKKEKGRAIVYEVSWRYEKGQPTLIGTSS</Hsp_hseq>
<Hsp_midline>D E++ ID L R F++ + + A +EV+ + T+ R K + G E QI + IPT+L N ++ +F + R I+ V+W+ E G+ T S</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
t/data/psiblast.xml view on Meta::CPAN
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>25.3102</Hsp_bit-score>
<Hsp_score>54</Hsp_score>
<Hsp_evalue>4.53564</Hsp_evalue>
<Hsp_query-from>291</Hsp_query-from>
<Hsp_query-to>317</Hsp_query-to>
<Hsp_hit-from>228</Hsp_hit-from>
<Hsp_hit-to>254</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>10</Hsp_identity>
<Hsp_positive>15</Hsp_positive>
<Hsp_align-len>27</Hsp_align-len>
<Hsp_qseq>KLSAKPADSLEISSNSPEIGKVVEAVL</Hsp_qseq>
<Hsp_hseq>ELKAKANQVVELNEKIPELNKATENVL</Hsp_hseq>
<Hsp_midline>+L AK +E++ PE+ K E VL</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
<Hit>
<Hit_num>19</Hit_num>
<Hit_id>gi|16411502|emb|CAD00110.1|</Hit_id>
<Hit_def>ftsZ [Listeria monocytogenes]</Hit_def>
<Hit_accession>CAD00110</Hit_accession>
<Hit_len>391</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>24.925</Hsp_bit-score>
<Hsp_score>53</Hsp_score>
<Hsp_evalue>6.28001</Hsp_evalue>
<Hsp_query-from>251</Hsp_query-from>
<Hsp_query-to>296</Hsp_query-to>
<Hsp_hit-from>159</Hsp_hit-from>
<Hsp_hit-to>204</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>14</Hsp_identity>
<Hsp_positive>21</Hsp_positive>
<Hsp_align-len>46</Hsp_align-len>
<Hsp_qseq>DTTSLIPQESKTEIVVNTKEFLQAIDRASLLAREGRNNVVKLSAKP</Hsp_qseq>
<Hsp_hseq>DTLIVIPNDRLLQIVDKNTPMLEAFREADNVLRQGVQGISDLIAVP</Hsp_hseq>
<Hsp_midline>DT +IP + +IV L+A A + R+G + L A P</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>2846</Statistics_db-num>
<Statistics_db-len>870878</Statistics_db-len>
<Statistics_hsp-len>82</Statistics_hsp-len>
<Statistics_eff-space>1.88702e+08</Statistics_eff-space>
<Statistics_kappa>0.0450367</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
<Iteration_message>CONVERGED</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
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