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

Gatherer, D. (Derek)
Wed, 22 Mar 2000 13:29:45 +0100

I'd like to ask list members what they think would be useful for a  This would use Peter Schattner's to
generate a codon table, and then have further methods to calculate the codon
bias statistics.  There are really 2 questions:

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

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

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