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: biojava-l@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) <[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 - Biojava-l@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/
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