Skip to main content
SpringerLink
Log in
Book cover

Annual Symposium on Combinatorial Pattern Matching

CPM 1995: Combinatorial Pattern Matching pp 128–143Cite as

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

Extended abstract

  • Conference paper
  • First Online:

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

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

This is a preview of subscription content, log in via an institution.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. S. F. Altschul. Gap costs for multiple sequence alignment. J. Theor. Biol., 138:297–309, 1989.

    PubMed  Google Scholar 

  2. S. F. Altschul, Raymond J. Carroll, and David J. Lipman. Weights for data related by a tree. J. Molecular Biology, 207:647–653, 1989.

    Article  Google Scholar 

  3. G. J. Barton and M. J. E. Sternberg. Evaluation and improvements in the automatic alignment of protein sequences. J. Mol. Biol., 198:327–337, 1987.

    PubMed  Google Scholar 

  4. G. J. Barton and M. J. E. Sternberg. A strategy for the rapid multiple alignment of protein sequences. Protein Engineering, 1:89–94, 1987.

    PubMed  Google Scholar 

  5. H. Bodlaender, R. G. Downey, M. R. Fellows, and H. T. Wareham. The parameterized complexity of sequence alignment and consensus. In Proc. of the 5th Symp. on Combinatorial Pattern Matching, Lecture Notes Comp. Sci. 807, pages 15–30, 1994.

    Google Scholar 

  6. H. Carrillo and D. Lipman. The multiple sequence alignment problem in biology. SLAM J. Appl. Math., 48:1073–1082, 1988.

    Article  Google Scholar 

  7. S. C. Chan, A. K. C. Wong, and D. K. Y. Chiu. A survey of multiple sequence comparison methods. Bulletin of Mathematical Biology, 54:563–598, 1992.

    PubMed  Google Scholar 

  8. E. W. Dijkstra. A note on two problems in connexion with graphs. Numerische Mathematik, 1:269–271, 1959.

    Article  Google Scholar 

  9. D. Feng and R. Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Molecular Evol., 25:351–360, 1987.

    Google Scholar 

  10. D. G. Higgins, A. J. Bleasby, and R. Fuchs. Clustal v: improved software for multiple sequence alignment. CABIOS, 8:189–191, 1992.

    PubMed  Google Scholar 

  11. J. Kececioglu. Notes on an approach of Carrillo and Lipman to minimum sum of pairs multiple sequence alignment. Unpublished notes, 1989.

    Google Scholar 

  12. J. Kececioglu. The maximum weight trace problem in multiple sequence alignment. In Proc. of the 4th Symp. on Combinatorial Pattern Matching, Springer-Verlag Lecture Notes in Comp. Sci. 684, pages 106–119, 1993.

    Google Scholar 

  13. D. J. Lipman, S. F. Altschul, and J. D. Kececioglu. A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA., 86:4412–4415, 1989.

    PubMed  Google Scholar 

  14. D. Maier. The complexity of some problems on subsequences and supersequences. J. ACM, 25:322–336, 1978.

    Article  Google Scholar 

  15. M. A. McClure, T. K. Vasi, and W. M. Fitch. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol., 11:571–592, 1994.

    PubMed  Google Scholar 

  16. S. Subbiah and S. C. Harrison. A method for multiple sequence alignment with gaps. J. Mol. Biol., 209:539–548, 1989.

    PubMed  Google Scholar 

  17. W. R. Taylor. Multiple sequence alignment by a pairwise algorithm. CABIOS, 3:81–87, 1987.

    PubMed  Google Scholar 

  18. W. R. Taylor. A flexible method to align large numbers of biological sequences. Journal of Molecular Evolution, 28:161–169, 1988.

    PubMed  Google Scholar 

  19. L. Wang and T. Jiang. On the complexity of multiple sequence alignment. J. Computational Biology, 1:337–348, 1994.

    Google Scholar 

Download references

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John D. Kececioglu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alejandro A. Schäffer
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Zvi Galil Esko Ukkonen

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

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

Download citation

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

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-60044-2

  • Online ISBN: 978-3-540-49412-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation