GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Chen Chen, Bertil Schmidt, Liu Weiguo, Wolfgang Muller-Wittig
School of Computer Engineering, Nanyang Technological University, Singapore
Pattern Recognition in Bioinformatics (2008), pp. 448-459


   title={GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences},

   author={Chen, C. and Schmidt, B. and Weiguo, L. and M{\”u}ller-Wittig, W.},

   journal={Pattern Recognition in Bioinformatics},





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Discovery of motifs that are repeated in groups of biological sequences is a major task in bioinformatics. Iterative methods such as expectation maximization (EM) are used as a common approach to find such patterns. However, corresponding algorithms are highly compute-intensive due to the small size and degenerate nature of biological motifs. Runtime requirements are likely to become even more severe due to the rapid growth of available gene transcription data. In this paper we present a novel approach to accelerate motif discovery based on commodity graphics hardware (GPUs). To derive an efficient mapping onto this type of architecture, we have formulated the compute-intensive parts of the popular MEME tool as streaming algorithms. Our experimental results show that a single GPU allows speedups of one order of magnitude with respect to the sequential MEME implementation. Furthermore, parallelization on a GPU-cluster even improves the speedup to two orders of magnitude.
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