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

[Gatherer, D. (Derek)]

-----Original Message-----
From: John Peden [mailto:johnp@molbiol.ox.ac.uk]
Sent: 22 March 2000 18:05
To: Gatherer, D. (Derek); bioperl guts;
vsns-bcd-perl@lists.uni-bielefeld.de
Subject: RE: Bioperl-guts: codon bias modules - what should be in them?

>I would be against including Codon Adaptation Index which must be one of
the
>most misused codon indices around, the index is good but people try to
apply
>it incorrectly to the wrong datasets (and they still manage to get it
>published in Science).

Right.

>I would avoid any index that implies prior knowledge of optimal codon
choice
>as these are species specific, and we only known this choice for very few
>species and it including them would seem to imply that someone would have
to
>maintain the module with lists of optimal codons.

Absolutely, I don't want to have to do that!!

>I consider Nc as superseding Scaled Chi square and derivatives, its just as
>or more accurate (Comeron and Aguade 1998 J Mol Evol 47:268-274) and is
less
>length dependent, so I would just include Nc.

I must read this article.  I always thought that SCS was length independent,
since the number of codons goes on the bottom line, but maybe Comeron and
Aguade can convince me otherwise.

>The P2 statistic is quite old and I don't see it as having a general
>application to codon bias.

Right.

>I am unfamiliar with "Shannon triplet informational entropy and redundancy"
>as applied to codon bias I see it more as a genome survey or gene discovery
>tool than codon bias method.

It's just that highly biased genes exhibit low entropy.

>So I would suggest a single module with light methods.

>these indices are genetic code dependent so this needs to
>be coded for as well.

aha!  Do we have a module that already handles this??

Cheers
Derek
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