[Biojava-l] Use Of Blosum62

[Andreas Dräger]

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