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

Some notes and diagrams about how it works. A few explanatory slides.

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

Go to the Dictionary of Algorithms and Data Structures home page.

If you have suggestions, corrections, or comments, please get in touch with Paul Black.

Entry modified 13 March 2006.
HTML page formatted Wed Mar 13 12:42:46 2019.

Cite this as:
Paul E. Black, "Smith-Waterman algorithm", in Dictionary of Algorithms and Data Structures [online], Paul E. Black, ed. 13 March 2006. (accessed TODAY) Available from: