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.
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Schröder, J., Wienbrandt, L., Pfeiffer, G., Schimmler, M. (2008). Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA. In: Chetty, M., Ngom, A., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2008. Lecture Notes in Computer Science(), vol 5265. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88436-1_37
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DOI: https://doi.org/10.1007/978-3-540-88436-1_37
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