Question: (Closed) Understanding a blast output
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gravatar for carolina.santiago.t
11 months ago by
carolina.santiago.t0 wrote:

enter code hereI performed a genome blast and saved the results for each chromosome in a .xml file. For each gene, 5 hitlist_size were defined. In the xml output file in the end of those 5 hits there is a <statistics> section. Can anyone help me understand the meaning of this section please? Below there is an exemple of the <statistics> i talked before. And then an entire <iteration>. Thank you in advance!

<iteration_stat> <statistics> <statistics_db-num>11969222</statistics_db-num> <statistics_db-len>4175987632</statistics_db-len> <statistics_hsp-len>140</statistics_hsp-len> <statistics_eff-space>670079475936</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> <iteration_iter-num>72</iteration_iter-num> <iteration_query-id>Query_72</iteration_query-id> <iteration_query-def>lcl|126619-127842, strand 0, homologs YNR021W</iteration_query-def> <iteration_query-len>1224</iteration_query-len> <iteration_hits> <hit> <hit_num>1</hit_num> <hit_id>emb|CCE90067.1|</hit_id> <hit_def>hypothetical protein TDEL_0A07350 [Torulaspora delbrueckii]</hit_def> <hit_accession>CCE90067</hit_accession> <hit_len>407</hit_len> <hit_hsps> <hsp> <hsp_num>1</hsp_num> <hsp_bit-score>786.178</hsp_bit-score> <hsp_score>2029</hsp_score> <hsp_evalue>0</hsp_evalue> <hsp_query-from>1</hsp_query-from> <hsp_query-to>1221</hsp_query-to> <hsp_hit-from>1</hsp_hit-from> <hsp_hit-to>407</hsp_hit-to> <hsp_query-frame>1</hsp_query-frame> <hsp_hit-frame>0</hsp_hit-frame> <hsp_identity>406</hsp_identity> <hsp_positive>407</hsp_positive> <hsp_gaps>0</hsp_gaps> <hsp_align-len>407</hsp_align-len> <hsp_qseq>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSEMNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVXXXXXXXXXXXXXXXXXXXXXXTGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_qseq> <hsp_hseq>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSELNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVEREMAQEKKQEAEKEKRRQLKATGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_hseq> <hsp_midline>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSE+NQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVEREMAQEKKQEAEKEKRRQLKATGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_midline> </hsp> </hit_hsps> </hit> <hit> <hit_num>2</hit_num> <hit_id>emb|CAR27877.1|</hit_id> <hit_def>ZYRO0D08668p [Zygosaccharomyces rouxii]</hit_def> <hit_accession>CAR27877</hit_accession> <hit_len>405</hit_len> <hit_hsps> <hsp> <hsp_num>1</hsp_num> <hsp_bit-score>459.914</hsp_bit-score> <hsp_score>1182</hsp_score> <hsp_evalue>7.17448e-159</hsp_evalue> <hsp_query-from>1</hsp_query-from> <hsp_query-to>1221</hsp_query-to> <hsp_hit-from>1</hsp_hit-from> <hsp_hit-to>405</hsp_hit-to> <hsp_query-frame>1</hsp_query-frame> <hsp_hit-frame>0</hsp_hit-frame> <hsp_identity>233</hsp_identity> <hsp_positive>309</hsp_positive> <hsp_gaps>2</hsp_gaps> <hsp_align-len>407</hsp_align-len> <hsp_qseq>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSEMNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVXXXXXXXXXXXXXXXXXXXXXXTGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_qseq> <hsp_hseq>MSGLLAPVLKLSELVNSFNDEYVSTPYEELKQMTILQRLSRYNWTFEIGGILVIAIVFALYKLGLYYNTRMTDGLFTQLNDYFKNDQQFARVGFANKDGSKLQYLDEQQKTWFTTFATGRSAVESICVRAHLYGRSNPAAMLMERLLGTFFP-SMTVKDLDEYCEIVVKPNGIYVANETAKPNANVSDILNNFKFVTSVVHKSSMNEVRRDNYYLSLTRTTESAKLPVEYVYMSEMNQLNEFISHYA-PNFFQVLREASSILHCISFTDLPTEKPLTEKKWNANLLPRAVIRTSIPSNKAQFKALKDVIGSVIAVYDNFTKDLVQKNPHVFITNDLLKKTSQLRSQELAKIVKTMKQVEREMALEKKHEAEKEQRRLLKQSGDAEKFDQKKRDRRERRAKNKQKVRM</hsp_hseq> <hsp_midline>MS L P++K + V + N +Y++ +EE K MT ++RL YNWTFEI + ++ +VF YK G+ N LF LN + ++D QFARVGF+ DGSK+ Y++E QKTW+TTFATGRSA+ S+ VR H++ RSNP AMLME L+ FP SMTVKD+ EYCE+V+KPNG +V++ETAKPN + D++N FKF+TS+V+KSSMNE+RR+NYYLSLT T+ES KLPVEYV+MSEMNQLN F HYA F ++L+ A + L I FTDLP KPLT+K W+A PRAVIRT IP ++ LK+++ +V+ ++DN T+++VQK+P FI +D+LKK++QLR+QELA+IVK MKQVEREMA EKK EAEKE+RR LK +G+ EKFDQK +++RERR +NKQKVRM</hsp_midline> </hsp> </hit_hsps> </hit> <hit> <hit_num>3</hit_num> <hit_id>gb|AQZ13762.1|</hit_id> <hit_def>YNR021W [Zygosaccharomyces parabailii]</hit_def> <hit_accession>AQZ13762</hit_accession> <hit_len>405</hit_len> <hit_hsps> <hsp> <hsp_num>1</hsp_num> <hsp_bit-score>455.677</hsp_bit-score> <hsp_score>1171</hsp_score> <hsp_evalue>3.27628e-157</hsp_evalue> <hsp_query-from>1</hsp_query-from> <hsp_query-to>1221</hsp_query-to> <hsp_hit-from>1</hsp_hit-from> <hsp_hit-to>405</hsp_hit-to> <hsp_query-frame>1</hsp_query-frame> <hsp_hit-frame>0</hsp_hit-frame> <hsp_identity>232</hsp_identity> <hsp_positive>313</hsp_positive> <hsp_gaps>2</hsp_gaps> <hsp_align-len>407</hsp_align-len> <hsp_qseq>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSEMNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVXXXXXXXXXXXXXXXXXXXXXXTGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_qseq> <hsp_hseq>MGSILAPLGKVGAYVNSLNKEYFTHSYEELKELGFVRRVRLYNWSFELCALLVCAVVYAFYKVGLFINSRRADRLFTEVNDYLKNNEQFARVGFAHKDGSKLQYLDERQKTWFTTFATGRSAIESVCMRMHMYGRSNPVAMLVERLLYNFFP-SLVIRDIEEYCEIVVRPNGIYVANEAAKPNTNITEVLNNFKFVTSIVNKSSMNEVRHDNYYLSLTRTSESSKLPLEYVYMSEMNQLNDFISFYC-PNFTNILQKASGILQCISFTDLPADKPLTDKVWNSNLQPRAVIRTSIPTSDSDIQALEQVISLVIAVYDNFTKDVVQGNPNTFVTHDLLKKTSLLRSQELAKIVKTMKQVEREMAIEKKQEAEKEKRRLLKHSGEQEKSDQKKKDRRERRAKNKQKVRM</hsp_hseq> <hsp_midline>M + L P+ K V +LN +Y ++EE K + FV R+R YNW+FE+ AL + +V+ YK G+ +N RA +LF +N +L+++ QFARVGF+ DGSK+ Y++E QKTW+TTFATGRSAI S+ +R+HM+ RSNPVAML+E L+ FP S+ ++D+ EYCE+V++PNG +V++E AKPN + +V+N FKF+TSIVNKSSMNE+R +NYYLSLT TSES KLP+EYV+MSEMNQLN F Y F +L++A LQ I FTDLPA+KPLTDK+W++ +PRAVIRT IP S+ D+ L++++S V+ ++DN T+++VQ +P F+ D+LKK++ LR+QELA+IVK MKQVEREMA EKKQEAEKEKRR LK +GEQEK DQK K++RERR +NKQKVRM</hsp_midline> </hsp> </hit_hsps> </hit> <hit> <hit_num>4</hit_num> <hit_id>gb|AQZ18210.1|</hit_id> <hit_def>YNR021W [Zygosaccharomyces parabailii]</hit_def> <hit_accession>AQZ18210</hit_accession> <hit_len>405</hit_len> <hit_hsps> <hsp> <hsp_num>1</hsp_num> <hsp_bit-score>454.521</hsp_bit-score> <hsp_score>1168</hsp_score> <hsp_evalue>9.24282e-157</hsp_evalue> <hsp_query-from>1</hsp_query-from> <hsp_query-to>1221</hsp_query-to> <hsp_hit-from>1</hsp_hit-from> <hsp_hit-to>405</hsp_hit-to> <hsp_query-frame>1</hsp_query-frame> <hsp_hit-frame>0</hsp_hit-frame> <hsp_identity>232</hsp_identity> <hsp_positive>312</hsp_positive> <hsp_gaps>2</hsp_gaps> <hsp_align-len>407</hsp_align-len> <hsp_qseq>MSAFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSEMNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVXXXXXXXXXXXXXXXXXXXXXXTGEQEKFDQKMKEKRERRLRNKQKVRM</hsp_qseq> <hsp_hseq>MGSILASLGKVGAYVNSLNKEYFSHSYEELKELGFVRRVRLYNWSFELCALLVCAIVYAFYKVGLFINSRRANRLFTQVNDYLKNDEQFARVGFAHKDGSKQLYLDERQKTWFTTFATGRSAIESVCMRVHMYGRSNPVAMLVERLLYTFFP-SLVIRDIEEYCDIVVRPNGIYVANEAAKPNTNITEVLNNFKFVTSIVNKSSMNEVRHDNYYLSLTRTSESSKLPLEYVYMSEMNQLNDFISFYC-PNFTNVLQKASGILQCISFTDLPADKPLTDKVWNSNLQPRAVIRTSIPTSDSDIQALEQVISLVIAVYDNFTKDVVQGNPNTFVTHDLLKKTSLLRSQELAKIVKTMKQVEREMAIEKKQEAEKEKRRLLKHSGEQEKSDQKKKDRRERRAKNKQKVRM</hsp_hseq> <hsp_midline>M + L + K V +LN +Y + ++EE K + FV R+R YNW+FE+ AL + +V+ YK G+ +N RA +LF +N +L++D QFARVGF+ DGSK Y++E QKTW+TTFATGRSAI S+ +RVHM+ RSNPVAML+E L+ FP S+ ++D+ EYC++V++PNG +V++E AKPN + +V+N FKF+TSIVNKSSMNE+R +NYYLSLT TSES KLP+EYV+MSEMNQLN F Y F +L++A LQ I FTDLPA+KPLTDK+W++ +PRAVIRT IP S+ D+ L++++S V+ ++DN T+++VQ +P F+ D+LKK++ LR+QELA+IVK MKQVEREMA EKKQEAEKEKRR LK +GEQEK DQK K++RERR +NKQKVRM</hsp_midline> </hsp> </hit_hsps> </hit> <hit> <hit_num>5</hit_num> <hit_id>emb|SCU87900.1|</hit_id> <hit_def>LAMI_0D07954g1_1 [Lachancea mirantina]</hit_def> <hit_accession>SCU87900</hit_accession> <hit_len>407</hit_len> <hit_hsps> <hsp> <hsp_num>1</hsp_num> <hsp_bit-score>419.083</hsp_bit-score> <hsp_score>1076</hsp_score> <hsp_evalue>8.72113e-143</hsp_evalue> <hsp_query-from>7</hsp_query-from> <hsp_query-to>1221</hsp_query-to> <hsp_hit-from>2</hsp_hit-from> <hsp_hit-to>407</hsp_hit-to> <hsp_query-frame>1</hsp_query-frame> <hsp_hit-frame>0</hsp_hit-frame> <hsp_identity>210</hsp_identity> <hsp_positive>301</hsp_positive> <hsp_gaps>5</hsp_gaps> <hsp_align-len>408</hsp_align-len> <hsp_qseq>AFLQPIIKGMDKVTALNAKYLALTFEEQKNMTFVERLRFYNWTFEIFALAMLVLVFVAYKYGVIVNENRAKKLFGSLNSFLQDDLQFARVGFSKGDGSKVPYIEEGQKTWYTTFATGRSAIASLSVRVHMFSRSNPVAMLMESLVNLMFPSSMTVKDVSEYCEVVIKPNGTFVSSETAKPNNDAKDVVNKFKFITSIVNKSSMNELRRENYYLSLTHTSESDKLPVEYVFMSEMNQLNGFTLHYADAGFNELLKRAGNFLQSICFTDLPANKPLTDKLWDATQKPRAVIRTKIPVSEQDLSLLKELVSAVVQIFDNVTREIVQKSPQAFINSDILKKSNQLRTQELARIVKAMKQVXXXXX--XXXXXXXXXXXXXXXXXTG-EQEKFDQKMKEKRERRLRNKQKVRM</hsp_qseq> <hsp_hseq>SILDPLLKALEFVNQLNAKYFALSYEEQKAMTFLERLQAYNWTFELVVVAILVLMYVFYVGGTKLNTRRASKLFGAINESFHE-LAFAKVGFSTKGGQKKQFISEQNNTWFTSFTTGRSAIESITVQSHMYAHYNPIAMLVERLLAVFFPA-LVERDLKEFVDICVMPNGIYASTETGEASKNADEVLSNFKFVTAVVNKSDMAKVREENYYLSITHTAENDKLPVQYVFMSENNQLNGLIPHYGGSRLHELLEKVGHFLTFISFTDLPEEKPVSDKLWEKAQKPRCVIRCKLQTNAADLKLLQELISCVVGMYDTMTREYVQGTAAPYLSKDLLKKSHQLRSQELQKIQKVMKQVERELAIEKKQKLEKEKRREQRSRLSGEEQDKLDKKMREKRERRQRNKQKTRM</hsp_hseq> <hsp_midline>+ L P++K ++ V LNAKY AL++EEQK MTF+ERL+ YNWTFE+ +A+LVL++V Y G +N RA KLFG++N + L FA+VGFS G K +I E TW+T+F TGRSAI S++V+ HM++ NP+AML+E L+ + FP+ + +D+ E+ ++ + PNG + S+ET + + +A +V++ FKF+T++VNKS M ++R ENYYLS+THT+E+DKLPV+YVFMSE NQLNG HY + +ELL++ G+FL I FTDLP KP++DKLW+ QKPR VIR K+ + DL LL+EL+S VV ++D +TRE VQ + +++ D+LKKS+QLR+QEL +I K MKQVERE+A +++K E EK + ++ + +G EQ+K D+KM+EKRERR RNKQK RM</hsp_midline> </hsp> </hit_hsps> </hit> </iteration_hits> <iteration_stat> <statistics> <statistics_db-num>11969222</statistics_db-num> <statistics_db-len>4175987632</statistics_db-len> <statistics_hsp-len>140</statistics_hsp-len> <statistics_eff-space>670079475936</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>

blast xml • 180 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by carolina.santiago.t0

Hello carolina.santiago.t!

We believe that this post does not fit the main topic of this site.

Duplicate

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 11 months ago by lakhujanivijay5.0k
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