Question: Understanding a blast output
0
gravatar for carolina.santiago.t
9 months ago by
carolina.santiago.t0 wrote:

I 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 • 213 views
ADD COMMENTlink modified 9 months ago by lakhujanivijay4.8k • written 9 months ago by carolina.santiago.t0

did you had a look at the webpage where the blast statistics are explained?

ADD REPLYlink written 9 months ago by lieven.sterck7.3k
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