[BiO BB] A question on Smith-Waterman algorithm

[Skull Crossbones]

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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