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

Bill Stephens grapeguy at gmail.com
Mon Oct 18 11:52:03 EDT 2010


Chris,

Well, That explains it.

I'll take a 2 pronged approach:
1. Try SimpleAlign
2. Driving the Mobyle UI using LWP::UserAgent, HTML::Form and
HTML::TableExtract (I do this for Tm calculations);

Thanks,
Bill S.



On Mon, Oct 18, 2010 at 10:54 AM, Chris Fields <cjfields at illinois.edu>wrote:

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 latest BioPerl-Run releases b/c the remote service is no longer active;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