[Biojava-l] Translation tables and Met

[Matthew Pocock]

Emig, Robin wrote:

> 4) What about the idea of just creating a new object called CodonBiasTable,
> which has all of these ideas added, plus the frequency weights? It could be
> based off of an internal translation table, and distribution.
> -Robin

You will get the most mileage out of the CodonBiasTable if it is 
something as simple as:

public interface CodonBiasTable {
   // translates codons to protein
   TranslationTable getTranslationTable();

   // codon bias table
   //
   // 2nd order distribution of p(aa | codon)
   Distribution<codonXprotein> getCodonBias();

   // joint distribition
   //
   // 2nd order distribution of p(aa && codon)
   Distribution<codonXprotein> getJointProbability();
}

This way, you can build a pair HMM using the joint probability, or can 
probablisticaly generate CDS given that you already know the protein 
sequence using the codonBias table. I guess the two probabilities are 
related. I will pop in a couple of utility classes into 
org.biojava.bio.dist

Does this sound sensible?

Matthew