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In biopython, how can i get the 100% identity aligment?

I find the way to get the identity of hsp ,but no alignment.One alignment can have multiple hsp, that means the score(identity) of hsp is no equal to alignment. when i do blast in webpage, i always get scores and identities of alignments. Is that any logical problem i made, who can explain this?

blast hsp identity biopython
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updated by Ram Ram • written by wuzongze001 • wuzongze001

1 answer

BLAST is a local alignment tool - it reports segments of the sequence, called HSPs, that align and produce the best scores. Each HSP in a match is a segment of query matching to a segment of the subject producing a high score. You can either use the meaningful maximum score or use a score totaled across all HSPs.

BLAST web UI has the same option - for identity percentage in case of multiple HSPs, it gives you the minimum identity% of the HSPs.

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written by Ram Ram

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