Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment.

S. K. Gupta, John D Kececioglu, A. A. Schäffer

Research output: Contribution to journalArticle

110 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. The MSA program implements a branch-and-bound technique together with 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. The improvements make feasible a variety of problem instances that were not feasible previously. On some runs we achieve an order of magnitude reduction in space usage and a significant multiplicative factor speedup in running time. To explain how these improvements work, we give a much more detailed description of MSA than has been previously available. In practice, MSA rarely produces a provably optimal alignment and we explain why.

Original languageEnglish (US)
Pages (from-to)459-472
Number of pages14
JournalJournal of Computational Biology
Volume2
Issue number3
StatePublished - Sep 1995
Externally publishedYes

Fingerprint

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. / Gupta, S. K.; Kececioglu, John D; Schäffer, A. A.

In: Journal of Computational Biology, Vol. 2, No. 3, 09.1995, p. 459-472.

Research output: Contribution to journalArticle

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