[Biojava-l] problem in alignment

[Andreas Dräger]

Dear Anant Jain,

Yeah, the problem is that the substitution matrices, e.g., BLOSUM 50,  
contain the *-symbol. So you'll definitely need the PROTEIN_TERM  
alphabet when doing protein alignments. Just try and let me know if it  
works.

Cheers
Andreas Dräger


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