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Optimal alignments in linear space.

E W Myers·W Miller
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Abstract

Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.

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AlgorithmsBase SequenceBiological EvolutionSequence Homology, Nucleic AcidSoftwareJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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E W Myers, W Miller. 1988. Optimal alignments in linear space.. https://doi.org/10.1093/bioinformatics%2F4.1.11

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