[Bioperl-l] Fwd: Need Help regarding reciprocal BLAST using BioPerl

shalabh sharma shalabh.sharma7 at gmail.com
Tue Oct 26 10:04:31 EDT 2010


Hey Sangita,
               I am not sure if bioperl has any direct command for
reciprocal blast.
But it is fairly simple, you can use all vs all blast then post process your
results in finding orthologs according to your cutoff parameters.

Other way is to use OrthoMCL :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/?tool=pubmed

Also read this:
http://bioperl.org/wiki/HOWTO:PhylogeneticAnalysisPipeline
 Since you are a beginner it will help you a lot.

Hope this helps.

Shalabh
-----------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
On Tue, Oct 26, 2010 at 7:41 AM, sangita saha <sahasangi at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: sangita saha <sahasangi at gmail.com>
> Date: Tue, Oct 26, 2010 at 4:32 PM
> Subject: Need Help regarding reciprocal BLAST using BioPerl
> To: bioperl-l at lists.open-bio.org
>
>
> Hello Sir,
> I have installed BioPerl and standalone BLAST in my PC.I faced problem in
> doing the Reciprocal BLAST.Will anyone kindly tell me how to link between
> BioPerl and Standalone BLAST ?How to use Bioperl itself to identify the
> ortholog?What is the command to be used for reciprocal Blast?Since I am the
> new user of it and need help to your concerned.If anybody have any
> experience regarding reciprocal blast please give me a suggestion.
>
> I will be happy to hear you from.
>
> Thank you
>
> With Regards,
> Sangita Saha
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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