Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA

Authors:
Jan Schröder;Lars Wienbrandt;Gerd Pfeiffer;Manfred Schimmler
Affiliations:
Department of Computer Science, Christian-Albrechts-University of Kiel, Germany;Department of Computer Science, Christian-Albrechts-University of Kiel, Germany;Department of Computer Science, Christian-Albrechts-University of Kiel, Germany;Department of Computer Science, Christian-Albrechts-University of Kiel, Germany
Venue:
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Year:
2008

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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.