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Smith-Waterman algorithm Created 2026-10-20 Updated 2026-11-05
The Smith-Waterman algorithm finds an optimal local sequence alignment for a specified additive scoring scheme. For a linear gap penalty , a dynamic programming score satisfiesZero permits an alignment to restart; tracing back from the largest entry to zero recovers a highest-scoring segment pair. Every optimal ending must have one of the listed final steps, which proves the recurrence by induction over the table. Optimality concerns this score, not guaranteed biological ancestry. [ref]
Identification of common molecular subsequences by Temple F. Smith and Michael S. Waterman. Smith and Waterman, 1981, Identification of common molecular subsequences
Temple F. Smith 2026-11-05
Temple F. Smith coauthored the algorithm for finding maximally similar segments within longer molecular sequences, now known as the Smith-Waterman algorithm. Its dynamic programming table permits a fresh start at score zero; a high-scoring segment can therefore begin and end inside either input rather than being forced to span both entire sequences.[ref]
Identification of common molecular subsequences by Temple F. Smith and Michael S. Waterman. Algorithm, equation 1 and traceback description, printed pp. 195–196
The zero option is a mechanistic part of the optimization: it discards a sufficiently unfavorable preceding alignment. Alignment traceback begins at a largest table entry and ends at zero. This supports finding a conserved region embedded within otherwise different sequences; the resulting similarity still requires biological interpretation rather than automatically proving a particular evolutionary history.