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

Chris Fields cjfields at illinois.edu
Tue Oct 26 11:40:02 EDT 2010


BioPerl does have Bio::Tools::Run::TribeMCL in BioPerl-Run, but I don't suggest using that.  mcl has a few tools in-place already within the distribition, but I personally have been using the latest version of OrthoMCL (v2), and have also started setting up a pipeline using InParanoid.

chris

On Oct 26, 2010, at 9:04 AM, shalabh sharma wrote:

> 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 at lists.open-bio.org
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>> 
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