Smith-Waterman algorithm


Definition: A means of searching protein databases to find those with the best alignment.

Aggregate child (... is a part of or used in me.)
dynamic programming.

Author: PEB


Ahmed Moustafa's implementation in JAligner (Java).

More information

Temple F. Smith and Michael S. Waterman, Identification of Common Molecular Subsequences, J. Mol. Biol., 147:195-197, 1981.

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Entry modified 14 December 2020.
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Cite this as:
Paul E. Black, "Smith-Waterman algorithm", in Dictionary of Algorithms and Data Structures [online], Paul E. Black, ed. 14 December 2020. (accessed TODAY) Available from: