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

Question

[wuzongze001]

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?

[Pierre Lindenbaum]

Hello wuzongze001!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/26767748

This is typically not recommended as it runs the risk of annoying people in both communities.

[wuzongze001]

I am sorry, I will not do it again.

[wuzongze001]

i will not do it again

Answer 1

[Ram]

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.

[wuzongze001]

Thank you, I understand it.