Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment

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

Research output: Contribution to journalArticle

111 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. 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
DOIs
StatePublished - Jan 1 1995
Externally publishedYes

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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