[Bioperl-l] Generating a consensus sequence from a Clustal alignment

Jun Yin jun.yin at ucd.ie
Mon Oct 18 12:09:32 EDT 2010


Hi, Bill,

You may consider to use consensus_iupac or consensus_string methods in
Bio::SimpleAlign to generate consensus sequence.

Cheers,
Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, October 18, 2010 3:55 PM
To: Bill Stephens
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

Bill,

Actually, the page you reached at Pasteur is not Pise, but Mobyle (their
replacement for the older Pise tools).  The Pise modules were in
BioPerl-Run, but they were deprecated a few years ago and removed from the
latest BioPerl-Run releases b/c the remote service is no longer active;
there is no Perl-based replacement for Mobyle interaction.  

Have you thought about just using the functionality within the
Bio::SimpleAlign class to generate the consensus?  I'm pretty sure there are
methods in place to do that.

chris

On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:

> All,
> 
> I'm in my first week with bioperl for a class project (although I've used
> Perl for years). I've successfully run a clustal alignment of several DNA
> sequences to produce the aln and dnd files. Now I would like to generate a
> consensus sequence from the alignment.  I see that Pise Cons does this
> satisfactorily on my example data (
> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
distribution
> that I installed.
> 
> Is this another module that I need to install separately?
> 
> "cpan[2]> m /Pise/
> Module    Bio::Tools::Run::AnalysisFactory::Pise
> (BIRNEY/bioperl-run-1.4.tar.gz)
> Module    Bio::Tools::Run::PiseApplication
(BIRNEY/bioperl-run-1.4.tar.gz)"
> 
> Bill S.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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