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

Albert Vilella avilella at gmail.com
Thu Aug 17 12:17:25 EDT 2006


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.
> >
> >
> > _______________________________________________
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> > 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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