-perc_query in local blast searches

Question

[karel.schoonvaere]

Dear all,

I was wondering whether there exists a flag for local blast commands that filters hits based on query coverage. Much like the -perc_identity 95 would only pass those hits with at least 95% identity between query and subject.

I'm using blast+ v2.2.31.

Thank you for your time

KS

Answer 1

[Siva]

Yes, there is an option to restrict hits based on query coverage.

-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp

[GenoMax]

That option is for query coverage per HSP. I think the OP wants a restriction over the full length of the query.

[karel.schoonvaere]

Thank you for the -qcov_hsp_perc Siva. I will try it out.

@genomax2, isn't HSP coverage and query coverage the same considering that I report only the highest scoring HSP (-max_hsps 1)? Might be wrong here...

[GenoMax]

If you are reporting only the highest scoring HSP then yes. I assume you are sure that the top HSP is all you want.