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)


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.


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.


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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

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