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. © 2008 Springer Berlin Heidelberg.
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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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5265 LNBI, pp. 436–447). Springer Verlag. https://doi.org/10.1007/978-3-540-88436-1_37
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