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Like the Needleman–Wunsch algorithm, of which it is a variation, Smith–Waterman is a dynamic programming algorithm. As such, it has the desirable property that it is guaranteed to find the optimal local alignment with respect to the scoring system being used (which includes the substitution matrix and the gap-scoring scheme).
The original purpose of the algorithm described by Needleman and Wunsch was to find similarities in the amino acid sequences of two proteins. [1] Needleman and Wunsch describe their algorithm explicitly for the case when the alignment is penalized solely by the matches and mismatches, and gaps have no penalty (d=0).
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Hirschberg's algorithm is simply described as a more space-efficient version of the Needleman–Wunsch algorithm that uses divide and conquer. [1] Hirschberg's algorithm is commonly used in computational biology to find maximal global alignments of DNA and protein sequences.
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Needleman–Wunsch algorithm; P. Probalign; S. Smith–Waterman algorithm This page was last edited on 21 April 2020, at 15:44 (UTC ...
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