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A fast homology program for aligning biological sequences.

P Taylor
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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.

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Amino Acid SequenceBase SequenceBiological EvolutionComputersDNAMinicomputersModels, GeneticProteinsSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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P Taylor. 1984-01-11. A fast homology program for aligning biological sequences.. https://doi.org/10.1093/nar%2F12.1part2.447

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