[BiO BB] A question on Smith-Waterman algorithm
marty.gollery at gmail.com
Thu Sep 14 12:36:52 EDT 2006
Yes, you can use an Identity matrix with nucleotide.
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
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Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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