[Biojava-l] Fwd: reverse translation

[Mark Schreiber]

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 <holland at eaglegenomics.com> 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) <John.Kneisler at uspto.gov>
> Date: 2008/8/28
> Subject: RE: [Biojava-l] reverse translation
> To: holland at eaglegenomics.com
>
>
> 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: dicknetherlands at gmail.com [mailto:dicknetherlands at gmail.com] On
> Behalf Of Richard Holland
> Sent: Tuesday, August 26, 2008 10:21 AM
> To: Kneisler, John (Raytheon)
> Cc: biojava-l at lists.open-bio.org
> Subject: Re: [Biojava-l] reverse translation
>
> Have you tried using the Protein-Term alphabet instead?
>
> cheers,
> Richard
>
> 2008/8/21 Kneisler, John (Raytheon) <John.Kneisler at uspto.gov>:
> > 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  -  Biojava-l at lists.open-bio.org
> > 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  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>