Hey Saif,
> FiniteAlphabet alphabet
> (FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");
>
This cannot work because the symbol "*" is indeed not included in the
alphabet "PROTEIN" as it marks the termination symbol. You will need to
use the alphabet "PROTEIN-TERM".
I hope that helps.
If I remember correctly, there have been discussions about that special
character in previous e-mails on that list.
Cheers,
Andreas
--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany
Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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