Hi - The best approach will be to use the CodonPref and SimpleCodonPref classes. These let you determine the frequency of all synonymous codons for a given amino acid.
There is a CodonPrefTools class that contains convenience methods and also has built in codon use tables for some common organisms. These classes are in the org.biojava.bio.symbol package. - Mark On 8/29/08, Richard Holland <[EMAIL PROTECTED]> wrote: > I've forwarded this to the list in case someone comes up with an > answer quicker than me. :) > > > ---------- Forwarded message ---------- > From: Kneisler, John (Raytheon) <[EMAIL PROTECTED]> > Date: 2008/8/28 > Subject: RE: [Biojava-l] reverse translation > To: [EMAIL PROTECTED] > > > Richard, > Thanks for your reply. I think I was using the Protein-Term > alphabet since I assigned a protein FiniteAlphabet variable to > ProteinTools.getTAlphabet(). The problem I am having is matching the > correct RNA alphabet to the correct protein alphabet. Here are the > runtime exceptions I am getting: > org.biojava.bio.symbol.IllegalAlphabetException: Couldn't create > translation table as the alphabets were different sizes: > 22:PROTEIN64:(RNA x RNA x RNA) > at > org.biojava.bio.symbol.SimpleReversibleTranslationTable.<init>(SimpleRev > ersibleTranslationTable.java:88) > > I have tried using the RNATools.getCodonAlphabet(); method to get an RNA > codon alphabet thinking that would match the protein alphabet when > assigning a translation table. Unfortunately my lack of experience and > understanding is showing. Any help would be appreciated. > > Thanks > John Kneisler > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Richard Holland > Sent: Tuesday, August 26, 2008 10:21 AM > To: Kneisler, John (Raytheon) > Cc: [email protected] > Subject: Re: [Biojava-l] reverse translation > > Have you tried using the Protein-Term alphabet instead? > > cheers, > Richard > > 2008/8/21 Kneisler, John (Raytheon) <[EMAIL PROTECTED]>: > > I am new to BioJava and I am trying to write a reverse translation > > function. Find the most probable DNA symbolList using a given a > > protein symbolList and a translation table. I tried using an RNA > > alphabet and protein alphabet and then I tried to use the > > SimpleReversibleTranslationTable's untranslate method and I got an > > "org.biojava.bio.symbol.IllegalAlphabetException: Couldn't create > > translation table as the alphabets were different sizes:". Is there > any > > way to create a reverse translation function using the BioJava > > framework? > > > > Thanks > > > > John > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > -- > Richard Holland > Finance Director > Eagle Genomics > http://www.eaglegenomics.com/ > > > > > > -- > Richard Holland > Finance Director > Eagle Genomics > http://www.eaglegenomics.com/ > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
