[BiO BB] A question on Smith-Waterman algorithm

[Martin Gollery]

Yes, you can use an Identity matrix with nucleotide.

Marty

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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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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