Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA

  • Jan Schröder
  • Lars Wienbrandt
  • Gerd Pfeiffer
  • Manfred Schimmler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5265)

Abstract

An enhanced version of an existing motif search algorithm BMA is presented. Motif searching is a computationally expensive task which is frequently performed in DNA sequence analysis. The algorithm has been tailored to fit on the COPACOBANA architecture, which is a massively parallel machine consisting of 120 FPGA chips. The performance gained exceeds that of a standard PC by a factor of over 1,650 and speeds up the time intensive search for motifs in DNA sequences. In terms of energy consumption COPACOBANA needs 1/400 of the energy of a PC implementation.

Keywords

Motif finding DNA sequence analysis FPGA High Performance Reconfigurable Computing (HPRC) 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Jan Schröder
    • 1
  • Lars Wienbrandt
    • 1
  • Gerd Pfeiffer
    • 1
  • Manfred Schimmler
    • 1
  1. 1.Department of Computer ScienceChristian-Albrechts-University of KielGermany

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