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

doi:10.1007/3-540-60044-2_39

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

Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings
Editors	Zvi Galil, Esko Ukkonen
Publisher	Springer-Verlag
Pages	128-143
Number of pages	16
ISBN (Print)	3540600442, 9783540600442
DOIs	https://doi.org/10.1007/3-540-60044-2_39
State	Published - Jan 1 1995
Event	6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995 - Espoo, Finland Duration: Jul 5 1995 → Jul 7 1995

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	937
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995
Country	Finland
City	Espoo
Period	7/5/95 → 7/7/95

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ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

Cite this

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

Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract). / Gupta, Sandeep K.; Kececioglu, John D.; Schäffer, Alejandro A.

Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings. ed. / Zvi Galil; Esko Ukkonen. Springer-Verlag, 1995. p. 128-143 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 937).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Gupta, SK, Kececioglu, JD & Schäffer, AA 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. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 937, Springer-Verlag, pp. 128-143, 6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995, Espoo, Finland, 7/5/95. https://doi.org/10.1007/3-540-60044-2_39

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

Gupta, Sandeep K. ; Kececioglu, John D. ; Schäffer, Alejandro A. / Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract). Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings. editor / Zvi Galil ; Esko Ukkonen. Springer-Verlag, 1995. pp. 128-143 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Access to Document

10.1007/3-540-60044-2_39