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Accelerating Motif Discovery: Motif Matching on Parallel Hardware

  • Geir Kjetil Sandve
  • Magnar Nedland
  • Øyvind Bø Syrstad
  • Lars Andreas Eidsheim
  • Osman Abul
  • Finn Drabløs
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

Abstract

Discovery of motifs in biological sequences is an important problem, and several computational methods have been developed to date. One of the main limitations of the established motif discovery methods is that the running time is prohibitive for very large data sets, such as upstream regions of large sets of cell-cycle regulated genes. Parallel versions have been developed for some of these methods, but this requires supercomputers or large computer clusters. Here, we propose and define an abstract module PAMM (Parallel Acceleration of Motif Matching) with motif matching on parallel hardware in mind. As a proof-of-concept, we provide a concrete implementation of our approach called MAMA. The implementation is based on the MEME algorithm, and uses an implementation of PAMM based on specialized hardware to accelerate motif matching. Running MAMA on a standard PC with specialized hardware on a single PCI-card compares favorably to running parallel MEME on a cluster of 12 computers.

Keywords

Expectation Maximization Motif Discovery Specialized Hardware Multiple Instruction Single Data Motif Position 
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 2006

Authors and Affiliations

  • Geir Kjetil Sandve
    • 1
  • Magnar Nedland
    • 2
  • Øyvind Bø Syrstad
    • 1
  • Lars Andreas Eidsheim
    • 1
  • Osman Abul
    • 3
  • Finn Drabløs
    • 3
  1. 1.Department of Computer and Information ScienceNorwegian University of Science and TechnologyTrondheimNorway
  2. 2.Interagon A.S.TrondheimNorway
  3. 3.Department of Cancer Research and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway

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