Question: Blastp filter by Identity
0
gravatar for sureshhewabi
12 months ago by
Sri Lanka
sureshhewabi0 wrote:

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 • 383 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum126k • written 12 months ago by sureshhewabi0
3
gravatar for lieven.sterck
12 months ago by
lieven.sterck6.9k
VIB, Ghent, Belgium
lieven.sterck6.9k wrote:

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 written 12 months ago by lieven.sterck6.9k

Thanks. I will check what is % positives

ADD REPLYlink written 12 months ago by sureshhewabi0
0
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

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 written 12 months ago by Pierre Lindenbaum126k

Thanks for the reply, BTW I am using TAB format

ADD REPLYlink written 12 months ago by sureshhewabi0
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