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)


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.


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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