Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):447-55.

A fast homology program for aligning biological sequences.

Abstract

The algorithm of Gotoh computes in two passes of MN steps the alignment of a pair of sequences of lengths M and N, subject to a constraint on the form of the gap weighting function. This compares with the previous algorithm of Waterman et al. which runs in M2N steps. Gotoh also gave a method using two passes of (L+2)MN steps in the case where gap weights remain constant for gaps of length greater than L. Here we describe a procedure for computing the alignment (evolutionary distance and optimal path) in a single pass of MN steps for both cases.

PMID:: 6546428; [PubMed - indexed for MEDLINE]
PMCID: PMC321061

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A fast homology program for aligning biological sequences.

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Cited by 11 PubMed Central articles

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