[Biojava-l] Fwd: reverse translation

Richard Holland holland at eaglegenomics.com
Fri Aug 29 08:08:34 UTC 2008

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

       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:

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.

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?


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
> way to create a reverse translation function using the BioJava
> framework?
> Thanks
> John
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Richard Holland
Finance Director
Eagle Genomics

Richard Holland
Finance Director
Eagle Genomics

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