Optimal alignments in linear space

EW Myers, W Miller - Bioinformatics, 1988 - academic.oup.com
Bioinformatics, 1988academic.oup.com
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 …
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.
Oxford University Press