[BiO BB] Running BLAST with a new scoring matrix

Dr. Achuthsankar S. Nair sankar.achuth at gmail.com
Fri Jul 29 00:10:59 EDT 2011

I have developed a new scoring matrix to replace PAM, can anyone suggest how
we can test this out in alignment tools inclusing BLAST ?
Is there a tool which accepts user defined  scoring matrix ?
Thanks in advance


Dr Achuthsankar S Nair
Director, State Inter-University  Centre for Bioinformatics
University of Kerala, Trivandrum 695581, INDIA
Tel (O) 471-2308759 (R) 471-2542220

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