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Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice

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Combinatorial Pattern Matching (CPM 1995)

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

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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.

Some of the work of this author was carried out at the Department of Computer Science of the University of California at Davis

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Author information

Author notes

  1. Sandeep K. Gupta

    Present address: Laboratory for Computer Science, Massachusetts Institute of Technology, 545 Technology Square, 02139, Cambridge, MA

Authors and Affiliations

  1. Department of Computer Science, Rice University, 77005-1892, Houston, TX

    Sandeep K. Gupta

  2. Department of Computer Science, The University of Georgia, 30602-7404, Athens, GA

    John D. Kececioglu

  3. Department of Computer Science, Rice University, 77005-1892, Houston, TX

    Alejandro A. Schäffer

Authors
  1. Sandeep K. Gupta
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  2. John D. Kececioglu
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  3. Alejandro A. Schäffer
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Editor information

Zvi Galil Esko Ukkonen

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© 1995 Springer-Verlag Berlin Heidelberg

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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. In: Galil, Z., Ukkonen, E. (eds) Combinatorial Pattern Matching. CPM 1995. Lecture Notes in Computer Science, vol 937. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-60044-2_39

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  • DOI: https://doi.org/10.1007/3-540-60044-2_39

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-60044-2

  • Online ISBN: 978-3-540-49412-6

  • eBook Packages: Springer Book Archive

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