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The Smith-Waterman algorithm performs local sequence alignment; that is, for
determining similar regions between two strings of nucleic acid sequences or
protein sequences. Instead of looking at the entire sequence, the
Smith-Waterman algorithm compares segments of all possible lengths and
optimizes the similarity measure. Gotoh and Atschul added optimizations making
it practical for larger problems.
WWW: https://github.com/ekg/smithwaterman
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