Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA

摘要

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 COPACODANA 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.