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
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