Design and implementation of a parallel architecture for biological sequence comparison

  • Pascale Guerdoux-Jamet
  • Dominique Lavenier
  • Charles Wagner
  • Patrice Quinton
Invited Talks
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1123)

Abstract

Samba is a full custom parallel hardware accelerator dedicated to the comparison of biological sequences. It implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty. The speed-up provided by Samba over standard workstations ranges from 50 to 500, depending on the application. Samba was designed with an effort of less than one person/year. This includes the design, fabrication and test of a full-custom Vlsi chip which is used as a building block for the 128 processor systolic array implementing the string alignment algorithm. We describe the Samba architecture, its performance characteristics, and we detail its design steps, from the initial specification to its full implementation. We report a first application of Samba to the study of yeast orphan sequences.

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References

  1. 1.
    S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman.-Basic local alignment search tool.-J. Mol. Biol, 215:403–410, 1990.PubMedGoogle Scholar
  2. 2.
    P. Bertin, D. Roncin, and J. Vuillemin.-Programmable active memories: a performance assessment.-In F. Meyer, B. Monien, and A.L. Rosenberg, editors, Parallel Architectures and their efficient use, pages 119–130. LNCS, Springer-Verlag, oct 1992.Google Scholar
  3. 3.
    E. Chow, T. Hunkapiller, and J. Peterson.-Biological Information Signal Processor.-In ASAP, pages 144–160, sep 1991.Google Scholar
  4. 4.
    Compugen.-The bioccelerator machine.-Israel, 1993.Google Scholar
  5. 5.
    O. Gotoh.-An Improved Algorithm for Matching Biological Sequences.-J. Mol. Biol., 162:705–708, 1982.PubMedGoogle Scholar
  6. 6.
    P. Guerdoux-Jamet and D. Lavenier.-Systolic filter for fast DNA similarity search.-In ASAP'95, Strasbourg, July 1995.Google Scholar
  7. 7.
    P. Guerdoux-Jamet and J.L. Risler.-Searching for a family to orphan sequences with SAMBA, a parallel hardware dedicated to biological applications.-Biochemistry, 1996.Google Scholar
  8. 8.
    D. Lavenier.-An Integrated 2D Systolic Array for Spelling Correction.-Integration: the VLSI journal, 15:97–111, August 1993.CrossRefGoogle Scholar
  9. 9.
    D. Lavenier.-Samba. Systolic Accelerators for Molecular Biological Applications.-Internal Publication 988, IRISA, Irisa, Campus de Beaulieu, 35042, Rennes-Cedex, France, April 1996.Google Scholar
  10. 10.
    D. Lopresty and al.-Building and using a highly parallel programmable logic array.-Computers, pages 81–89, jan 1991.Google Scholar
  11. 11.
    S.B. Needleman and C.D. Wunsh.-A General Method Applicable to the Search of Similarities in the Amino Acid Sequence of Two Proteins.-J. Mol. Biol, 48:443–453, 1970.PubMedGoogle Scholar
  12. 12.
    W. R. Pearson and D.J. Lipman.-Improved tools for biological sequence comparison.-Proc. Natl. Acad. Sci., 85:3244–3248, 1988.Google Scholar
  13. 13.
    W.R. Pearson.-Searching protein sequence libraries: comparison of the sensitivity and selectivity of the smith and waterman and fasta algorithms.-Genomics, 11:635–650, 1991.PubMedGoogle Scholar
  14. 14.
    F. Raimbault and D. Lavenier.-ReLaCS for Systolic Programming.-In ASAP'93, October 1993.Google Scholar
  15. 15.
    T.F. Smith and M.S. Waterman.-Identification of common molecular subsequences.-J. Mol. Biol, 147:195–197, 1981.PubMedGoogle Scholar
  16. 16.
    S.S. Sturrock and J.F. Collins.-Mpsearch version 1.3.-Technical report, University of Edinburgh, Biocomputing Research Unit, 1993.Google Scholar
  17. 17.
    M.S. Waterman.-Mathematical Methods for DNA Sequences.-CRC Press, Inc, 1989.Google Scholar
  18. 18.
    C.T. White, R.K. Singh, P.B. Reintjes, J. Lampe, B.W. Erickson, W.D. Dettloff, V.L. Chi, and S.F. Altschul.-BioSCAN: A VLSI-Based System for Biosequence Analysis.-In IEEE Int. Conf on Computer Design: VSLI in Computer and Processors, pages 504–509. IEEE Computer Society Press, oct 1991.Google Scholar

Copyright information

© Springer-Verlag 1996

Authors and Affiliations

  • Pascale Guerdoux-Jamet
    • 1
  • Dominique Lavenier
    • 1
  • Charles Wagner
    • 1
  • Patrice Quinton
    • 1
  1. 1.IrisaRennes CedexFrance

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