Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract)

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

Abstract

The MSA program, written and distributed in 1989, is one of the few existing programs that attempts to find optimal alignments of multiple protein or DNA sequences. MSA implements a branch-and-bound technique on a variant of Dijkstra's shortest paths algorithm to prune the basic dynamic programming graph. We have made substantial improvements in the time and space usage of MSA. On some runs, we achieve an order of magnitude reduction in space usage and a significant multiplicative factor speedup in running time. To explain these improvements, we give a much more detailed description of MSA than has been previously available.

Original languageEnglish (US)
Title of host publicationCombinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings
EditorsZvi Galil, Esko Ukkonen
PublisherSpringer-Verlag
Pages128-143
Number of pages16
ISBN (Print)3540600442, 9783540600442
DOIs
StatePublished - Jan 1 1995
Externally publishedYes
Event6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995 - Espoo, Finland
Duration: Jul 5 1995Jul 7 1995

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume937
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995
CountryFinland
CityEspoo
Period7/5/957/7/95

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Gupta, S. K., Kececioglu, J. D., & Schäffer, A. A. (1995). Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract). In Z. Galil, & E. Ukkonen (Eds.), Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings (pp. 128-143). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 937). Springer-Verlag. https://doi.org/10.1007/3-540-60044-2_39