Biostar Beta. Not for public use.
Blastp filter by Identity
0
Entering edit mode
19 months ago
Sri Lanka

I want to filter blast results by identity. I can find an option/parameter in blastn which is -perc_identity. but it is not available in blastp. I can get the blast result and the filter out results as a post process. but can't I do it by specifying a parameter like -perc_identity in blastp? why that option is missing?

BLAST 2.7.1+

sequence • 186 views
ADD COMMENTlink
3
Entering edit mode
6 months ago
VIB, Ghent, Belgium

I think it's mainly because identity does not mean much on protein level (at least not as it does for blastn, nucleotide level), for protein comparison % positives is more informative. Nonetheless that's also not an option for blastP though.

In general it's not the best approach to let blast "filter" your results (look around on biostar and/or internet for reasons why) , so doing it in post processing is the preferred way , and easily done with a bit of awk for instance

ADD COMMENTlink
0
Entering edit mode

Thanks. I will check what is % positives

ADD REPLYlink
0
Entering edit mode
16 months ago
France/Nantes/Institut du Thorax - INSE…

if you're using a xml output, using a xslt stylesheet, one can filter the Hsp on the identity.

xsltproc --novalid  biostar362495.xsl input.blastp.xml

ADD COMMENTlink
0
Entering edit mode

Thanks for the reply, BTW I am using TAB format

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1