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

[John Peden]

> a) Do we want everything in a single module or would it then be too heavy?

> b) What do we want in it anyway?
>
> Things that occur to me are:
>
> GC-3 (GC in 3rd position)
> Codon Adaptation Index
> Relative Synonymous Codon Usage
> Sharp's Scaled Chi Square, and derivatives
> Wright's Nc
> Gouy and Gautier's P2
> Shannon triplet informational entropy and redundancy

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).

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.

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.

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

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.

So I would suggest a single module with light methods.

 GC-3 (GC in 3rd position)
 Maybe GC skew also in the 3rd codon position
 Relative Synonymous Codon Usage
 Wright's Nc
 Maybe Shannon triplet informational entropy and redundancy

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


John

John Peden
MRC Haematology
IMM, Oxford, UK
+44 1865 222350








> These are purely a reflection of my former life as a codon bias
> nerd.  Maybe
> there is nobody else who is interested in this....
>
> Thanks in advance for any input
>
> Derek
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