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Smithwaterman

May 26, 2018

Smith-waterman-gotoh alignment algorithm

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