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 Citations (Scopus)

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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PublisherSpringer Verlag
Pages128-143
Number of pages16
Volume937
ISBN (Print)3540600442, 9783540600442
DOIs
StatePublished - 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)03029743
ISSN (Electronic)16113349

Other

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

Fingerprint

Multiple Sequence Alignment
DNA sequences
Dynamic programming
Shortest path
Proteins
Dijkstra Algorithm
Shortest Path Algorithm
Branch-and-bound
Protein Sequence
DNA Sequence
Dynamic Programming
Multiplicative
Alignment
Speedup
Graph in graph theory

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 937, 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.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 937 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 proceedingConference 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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 937, 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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 937. 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). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 937 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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