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The Location of the Gene Regions Under Selective Pressure: Plato Algorithm Parallelization

  • Yuri Vyatkin
  • Konstantin Gunbin
  • Alexey Snytnikov
  • Dmitry Afonnikov
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4671)

Abstract

The number of sequenced genes is dramatically increasing with that of international genomic projects. The gene sequence information proved to be helpful in predictions of protein structure, protein function and mutations targeted at improving the biological and biotechnological properties of proteins. Processing of the immense information stored in the databases demands high-throughput computational approaches. Here, we performed a parallelization of the algorithm for analysis of nucleotide substitutions in gene sequences from different organisms previously implemented in the PLATO program. The results demonstrated that the parallelization of the algorithm provides linear speedup of the PLATO program.

Keywords

gene evolution maximum likelihood algorithm parallel computing 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Yuri Vyatkin
    • 1
  • Konstantin Gunbin
    • 1
  • Alexey Snytnikov
    • 2
  • Dmitry Afonnikov
    • 1
  1. 1.Institure of Cytology and Genetics SB RAS, Lavrentyev aven., 10, 630090, NovosibirskRussia
  2. 2.Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Lavrentyev aven., 6, 630090, NovosibirskRussia

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