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Parallel CLUSTAL W for PC Clusters

  • James Cheetham
  • Frank Dehne
  • Sylvain Pitre
  • Andrew Rau-Chaplin
  • Peter J. Taillon
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2668)

Abstract

This paper presents a parallel version of CLUSTALW, called pCLUSTAL. In contrast to the commercial SGI parallel Clustal, which requires an expensive shared memory SGI multiprocessor, pCLUSTAL can be run on a range of distributed and shared memory parallel machines, from high-end parallel multiprocessors (e.g. Sunfire 6800, IBM SP2, etc.) to PC clusters, to simple networks of workstations. We have implemented pCLUSTAL using C and the MPI communication library, and tested it on a PC cluster. Our experimental evaluation shows that our pCLUSTAL code achieves similar or better speedup on a distributed memory PC clusters than the commercial SGI parallel Clustal on a shared memory SGI multiprocessor.

KeyWords

Multiple Sequence Alignment CLUSTALW Parallel Computing Computational Biochemistry 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • James Cheetham
    • 1
  • Frank Dehne
    • 2
  • Sylvain Pitre
    • 2
  • Andrew Rau-Chaplin
    • 3
  • Peter J. Taillon
    • 2
  1. 1.Institute of BiochemistryCarleton UniversityOttawaCanada
  2. 2.School of Computer ScienceCarleton UniversityOttawaCanada
  3. 3.Faculty of Computer ScienceDalhousie UniversityHalifaxCanada

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