[Biojava-l] Translation tables and Met

[Schreiber, Mark]

A codon bias table would also be good for making gene finding HMM's esp if
it included dicodon pairs, hint hint ;-)

Mark


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 

> -----Original Message-----
> From: Emig, Robin [mailto:Robin.Emig@maxygen.com]
> Sent: Thursday, August 30, 2001 4:23 AM
> To: 'Matthew Pocock'; Emig, Robin
> Cc: 'Keith James'; BioJava List
> Subject: RE: [Biojava-l] Translation tables and Met
> 
> 
> Sounds good, but I do like the idea of including start/stop 
> codons in the
> class.
> Robin
> 
> -----Original Message-----
> From: Matthew Pocock [mailto:mrp@sanger.ac.uk]
> Sent: Wednesday, August 29, 2001 3:09 AM
> To: Emig, Robin
> Cc: 'Keith James'; BioJava List
> Subject: Re: [Biojava-l] Translation tables and Met
> 
> 
> 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
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