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

Chris Fields cjfields at uiuc.edu
Thu Aug 17 10:26:33 EDT 2006


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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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