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  • Standalone Blast output

    Hi

    When looking at the output from standalone blast I see this:

    <Hsp_hit-from>76056</Hsp_hit-from>
    <Hsp_hit-to>76901</Hsp_hit-to>
    <Hsp_query-frame>0</Hsp_query-frame>
    <Hsp_hit-frame>3</Hsp_hit-frame>
    <Hsp_identity>89</Hsp_identity>
    <Hsp_positive>141</Hsp_positive>
    <Hsp_gaps>19</Hsp_gaps>
    <Hsp_align-len>286</Hsp_align-len>

    Can anyone tell me why is the align length less than "hit-to" minus "hit-from"?

    Is there a description of the output available anywhere, maybe I am looking at this wrongly. Hope you can help

    Thanks

  • #2
    Originally posted by jomaco View Post
    <Hsp_hit-from>76056</Hsp_hit-from>
    <Hsp_hit-to>76901</Hsp_hit-to>
    ...
    <Hsp_gaps>19</Hsp_gaps>
    <Hsp_align-len>286</Hsp_align-len>

    Can anyone tell me why is the align length less than "hit-to" minus "hit-from"?
    It looks like there are 19 gaps in the alignment (Hsp_gaps is non-zero), which will contribute substantially to the align length being shorter than the hit range.

    Is there a description of the output available anywhere
    ftp://ftp.ncbi.nlm.nih.gov/blast/doc...l/README.blxml

    Linked from the first google hit for "BLAST XML format".

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