Bioperl-guts: codon bias modules - what should be in them?

John Peden johnp@molbiol.ox.ac.uk
Thu, 23 Mar 2000 16:01:18 -0000



> >
> > aha!  Do we have a module that already handles this??
> >
>
> Yes. Heikki's excellent CodonTable.pm
>

Yes Heikki's module is an excellent starting point but to calculate these
indices we also need to know how many synomns a codon  (i.e. 6 4 3 2 or 1 )
has under each genetic code, also the number of synonyms used for each AA is
useful. Even something a trivial as GC3s (GC content at synonymous third
positions) is code dependent so the standard indexes need to tweaked if they
are going to be applied under alternative genetic codes. I already have the
necessary code in C if it is decided to include codon bias indices.



John








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