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

Jun Yin jun.yin at ucd.ie
Tue Oct 19 04:17:58 EDT 2010


Hi, Bill,

 

There are several methods you can choose from Bio::SimpleAlign to build
subalignment. For example, you can use $aln->slice  to get part of your
alignment, and then you can calculate concensus sequence from subalignment.
Another method $aln->remove_gaps, which can remove gap containing columns.

 

Cheers,

Jun Yin

Ph.D. student in U.C.D.

 

Bioinformatics Laboratory

Conway Institute

University College Dublin

 

From: Bill Stephens [mailto:grapeguy at gmail.com] 
Sent: Tuesday, October 19, 2010 1:03 AM
To: Jun Yin
Cc: Chris Fields; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Generating a consensus sequence from a Clustal
alignment

 

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latest BioPerl-Run releases b/c the remote service is no longer active;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