[Bioperl-l] Modifying Blast plus parameters

[Paul Cantalupo]

Hi Oz

I'm assuming that you are running a local blast, right? blastn has
-perc_identity option but none of the other programs (blastp, blastx,
etc...) have this option. As for maximal length, do you mean Query Coverage
like you get when doing a BLAST at NCBI (
http://blast.ncbi.nlm.nih.gov/Blast.cgi)? If so, there are two options in
blast that you can choose (from 'blastn -help'):

qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP

Then you would have to filter the blast output manually on your QC value
since the blast programs do not have an option for this.

Regards,

Paul







Paul Cantalupo
University of Pittsburgh


On Fri, Apr 25, 2014 at 2:21 AM, Oz <oz.sharabi at mail.huji.ac.il> wrote:

> Hi,
> I'm a new user of bioperl. So far, I used it to run default blast-plus
> alignments.
> However, I wanted to change a bit some parameters, but could not figure out
> how..
> I would like to limit the blast search by:
>
> 1. Percentage of identical nucleotides (not e-value).
> 2. Maximal length of the aligned sequence (when I run list of sequences
> with
> different lengths, this value varies so I can't use a constant).
> Can you please explain how can I do it?
>
> Thank you in advance,
> Oz
>
>
>
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