Optimal alignments in linear space

Comput Appl Biosci. 1988 Mar;4(1):11-7. doi: 10.1093/bioinformatics/4.1.11.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Base Sequence*
  • Biological Evolution
  • Sequence Homology, Nucleic Acid
  • Software