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

[Bill Stephens]

So, I've got the SimpleAlign running. It looks like it's running the
alignment based upon the input sequence location only (first residue from
each sequence).  This is not what I need.

I'm back to to clustal, tcoffee or dalign.

Bill

On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:

> 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 latest BioPerl-Run releases b/c the remote service is no longer active;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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