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
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 937)


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.


Multiple Sequence Alignment Priority Queue Pairwise Alignment Outgoing Edge Optimal Alignment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 1995

Authors and Affiliations

  • Sandeep K. Gupta
    • 1
  • John D. Kececioglu
    • 2
  • Alejandro A. Schäffer
    • 3
  1. 1.Department of Computer ScienceRice UniversityHouston
  2. 2.Department of Computer ScienceThe University of GeorgiaAthens
  3. 3.Department of Computer ScienceRice UniversityHouston

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