[Bioperl-l] informative codons method for kaks --Bio/Align/DNAStatistics.pm

Chris Fields cjfields at uiuc.edu
Thu Aug 17 12:39:19 EDT 2006


Albert,

Might be a good idea to start working on those!  Nice to use Bugzilla as a
repository for ideas, but we're heading towards using the Bioperl wiki for
that more now.

Chris

> -----Original Message-----
> From: Albert Vilella [mailto:avilella at gmail.com]
> Sent: Thursday, August 17, 2006 11:17 AM
> To: Chris Fields
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] informative codons method for kaks --
> Bio/Align/DNAStatistics.pm
> 
> I will opt for the "return the number of informative codons" then, which
> is the easiest :)
> 
> I don't know when is this going to be there if it depends on me,
> though... my list of 'enh' bug tickets is growing shamefully fast :p
> 
> Cheers,
> 
>     Albert.
> 
> On Thu, 2006-08-17 at 09:26 -0500, Chris Fields wrote:
> > Sure, why not?  If you (or someone) can add one in, I don't see how
> > it could hurt.
> >
> > Make sure to add tests for this in the proper test suite.
> >
> > Chris
> >
> > On Aug 17, 2006, at 6:37 AM, Albert Vilella wrote:
> >
> > > Hi all,
> > >
> > > I think it would be nice to have a method in
> > > Bio/Align/DNAStatistics.pm that gives the number of informative codons
> > > for kaks in a MSA. That is, the codons that are used in the
> > > calculation of kaks. This, AFAICS, more or less what codeml calls
> > > "patterns".
> > >
> > > I often find myself in the situation of wanting to know how big is the
> > > CDS alignment not in terms of sequence length, but of the number of
> > > codons that are going to be used in the kaks statistics. I guess this
> > > method would help in that.
> > >
> > > The method could:
> > >
> > > return the number of informative codons?
> > > maybe return a new seqarray with only the informative codons?
> > >
> > > What do you think? Jason? Chris?
> > >
> > > http://bugzilla.open-bio.org/show_bug.cgi?id=2078
> > >
> > > Bests,
> > >
> > >     Albert.
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
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> > Bioperl-l at lists.open-bio.org
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