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