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Comput Appl Biosci. 1988 Mar;4(1):11-7.

Optimal alignments in linear space.

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Department of Computer Science, University of Arizona, Tucson 85721.


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.

[Indexed for MEDLINE]

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