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
Bio::Tools:CodonBias.pm. This would use Peter Schattner's SeqStats.pm 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
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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