[BiO BB] A question on Smith-Waterman algorithm

Dr. Achuthsankar S. Nair sankar.achuth at gmail.com
Thu Sep 14 12:30:31 EDT 2006

When you use PAM and BLOSUM, the simple 1/0 scoring is no longer applicable,
they are overtaken by the PAM/BLOSUM matrices themselves
Dr Achuthsankar S Nair
Hon. Director
Centre for Bioinformatics
University of Kerala, Trivandrum 695581, INDIA
Tel (O) 471-2412759 (R) 471-2542220
Admissions to MPhil Bioinformatics for Jan 2007 Open - Brochure and
Application forms can be downloaded from www.cbi.keralauniversity.edu

On 9/14/06, Skull Crossbones <witch_of_agnessi at yahoo.com> wrote:
> Hello all,
> In the SW algo. mismatches are given negative scores.
> Does this mean I can not use an Identity Scoring
> Matrix ( 1 for match and 0 for mismatch) for aligning
> DNA sequences? Does the term "Mismatch" applies for
> protein scoring matrices like PAM and BLOSUM
> Thanks in advance
> WoA
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