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 | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
| Publisher | Springer Verlag |
| Pages | 128-143 |
| Number of pages | 16 |
| Volume | 937 |
| ISBN (Print) | 3540600442, 9783540600442 |
| DOIs | |
| State | Published - 1995 |
| Externally published | Yes |
| 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) | 03029743 |
| ISSN (Electronic) | 16113349 |
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
- Computer Science(all)
- Theoretical Computer Science
Cite this
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 proceeding › Conference contribution
}
TY - GEN
T1 - Making the shortest-paths approach to Sum-of-Pairs multiple sequence alignment more space efficient in practice (Extended Abstract)
AU - Gupta, Sandeep K.
AU - Kececioglu, John D
AU - Schäffer, Alejandro A.
PY - 1995
Y1 - 1995
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=3643075904&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=3643075904&partnerID=8YFLogxK
U2 - 10.1007/3-540-60044-2_39
DO - 10.1007/3-540-60044-2_39
M3 - Conference contribution
AN - SCOPUS:3643075904
SN - 3540600442
SN - 9783540600442
VL - 937
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 128
EP - 143
BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PB - Springer Verlag
ER -