Advertisement

Cache-Based Parallelization of Multiple Sequence Alignment Problem

  • Gilles Parmentier
  • Denis Trystram
  • Jaroslaw Zola
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3149)

Abstract

In this paper we present new approach to the problem of parallel multiple sequence alignment. The proposed method is based on the application of caching technique and is aimed to solve, with high precision, large alignment instances on the heterogeneous clusters. The cache is used to store partial alignment guiding trees which can be reused in future computations, and is applied to eliminate redundancy of computations in parallel environment. We describe an implementation based on the CaLi library, the software designed for caches implementation. We report preliminary experimental results and finally, we propose some extensions of our method.

Keywords

Multiple Sequence Alignment Multiple Alignment Distance Matrix Pairwise Alignment Neighborhood Determination 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Philips, A., Janies, D., Wheeler, W.: Multiple sequence alignment in phylogenetic analysis. Mol. Phyl. Evol. 16, 317–330 (2000)CrossRefGoogle Scholar
  2. 2.
    Sankoff, D., Morel, C., Cedergren, R.: Evolution of 5s rna and the nonrandomness of base replacement. Nature New Biology 245, 232–234 (1973)CrossRefGoogle Scholar
  3. 3.
    Jiang, T., Lawler, E., Wang, L.: Aligning sequences via an evolutionnary tree: Complexity and approximation. In: Proc. 26th Ann. ACM Symp. on Theory of Comp., pp. 760–769 (1994)Google Scholar
  4. 4.
    Guinand, F., Parmentier, G., Trystram, D.: Integration of multiple alignment and phylogeny reconstruction. In: Eur. Conf. on Comp. Biology, Poster Abstr. (2002)Google Scholar
  5. 5.
    Cao, P., Irani, S.: Cost-aware www proxy caching algorithms. In: USENIX Symposium on Internet Technologies and Systems, pp. 193–206 (1997)Google Scholar
  6. 6.
    Katoh, K., Misawa, K., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res. 30, 3059–3066 (2002)CrossRefGoogle Scholar
  7. 7.
    Lee, C., Grasso, C., Sharlow, M.: Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452–464 (2002)CrossRefGoogle Scholar
  8. 8.
    Morgenstern, B.: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211–218 (1999)CrossRefGoogle Scholar
  9. 9.
    Higgins, D., Thompson, J., Gibson, T.: CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)CrossRefGoogle Scholar
  10. 10.
    Pei, J., Sadreyev, R., Grishin, N.: PCMA: fast and accurate multiple alignment based on profile consistency. Bioinformatics 19, 427–428 (2003)CrossRefGoogle Scholar
  11. 11.
    Notredame, C., Henriga, D.G.H., T–Coffee, J.: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000)CrossRefGoogle Scholar
  12. 12.
    Iyer, S., Rowston, A., Druschel, P.: Squirrel: A decentralized, peer-to-peer web cache. In: 12th ACM Symp. on Princ. of Distr. Computing (2002)Google Scholar
  13. 13.
    CaLi – generic computational buffers library (2004), Web Page, http://icis.pcz.pl/~zola/CaLi
  14. 14.
    Sankoff, D.: Minimal mutation trees of sequences. SIAM J. Appl. Math. 28, 35–42 (1975)zbMATHCrossRefMathSciNetGoogle Scholar
  15. 15.
    Accord cluster (2003), Web Page http://eltoro.pcz.pl
  16. 16.
    Treebase – a database of phylogenetic knowledge (2004), Web Page http://www.treebase.org
  17. 17.
    Licklider, J.: Man-computer symbiosis. IRE Trans. on Hum. Fact. In: Elect. HFE–1, 4–11 (1960)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Gilles Parmentier
    • 1
  • Denis Trystram
    • 2
  • Jaroslaw Zola
    • 2
    • 3
  1. 1.Laboratoire LBMCEcole Normale Superieure of LyonFrance
  2. 2.Laboratoire ID IMAGFrance
  3. 3.Institute of Computer & Information SciencesCzestochowa University of TechnologyPoland

Personalised recommendations