[Biojava-l] Protein CharacterTokenization

mark.schreiber at novartis.com mark.schreiber at novartis.com
Sun Jul 24 21:42:32 EDT 2005

Hello -

Can you provide some example code?

Any protein ambiguity should map to X. Unlike DNA which has lots of 
ambiguity codes with different meanings. BioJava can support all kinds of 
protein ambiguity but when they are tokenized they should all end up as X.

- Mark

"Tal Blum" <tblum at andrew.cmu.edu>
Sent by: biojava-l-bounces at portal.open-bio.org
07/24/2005 10:14 AM

        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Protein CharacterTokenization


There is something strange with the protein alphabet 
It knows how to parse the ambiguity symbol 'X', but it does not contain 
other way around mapping of the protein alphabet ambiguity symbol to 'X'. 
that the way it should be or is that a bug?
Can someone suggest a way I can correct it? The Alphabet is wrapped in a
WellKnownTokenizationWrapper in AlphabetManager, so I can't simply add a
Symbol to it.

Thanks, tal

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