Question: -perc_query in local blast searches
0
gravatar for karel.schoonvaere
3.4 years ago by
Belgium
karel.schoonvaere0 wrote:

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

blast alignment • 1.0k views
ADD COMMENTlink modified 3.4 years ago by Siva1.6k • written 3.4 years ago by karel.schoonvaere0
0
gravatar for Siva
3.4 years ago by
Siva1.6k
United States
Siva1.6k wrote:

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

-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
ADD COMMENTlink written 3.4 years ago by Siva1.6k

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

ADD REPLYlink written 3.4 years ago by genomax66k

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...

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by karel.schoonvaere0

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

ADD REPLYlink written 3.4 years ago by genomax66k
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