3520

A Parallel Gibbs Sampling Algorithm for Motif Finding on GPU

Linbin Yu, Yun Xu
Dept. of Comput. Sci., Univ. of Sci. & Technol. of China, Hefei, China
IEEE International Symposium on Parallel and Distributed Processing with Applications, 2009

@conference{yu2009parallel,

   title={A Parallel Gibbs Sampling Algorithm for Motif Finding on GPU},

   author={Yu, L. and Xu, Y.},

   booktitle={2009 IEEE International Symposium on Parallel and Distributed Processing with Applications},

   pages={555–558},

   year={2009},

   organization={IEEE}

}

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Motif is overrepresented pattern in biological sequence and motif finding is an important problem in bioinformatics. Due to high computational complexity of motif finding, more and more computational capabilities are required as the rapid growth of available biological data, such as gene transcription data. Among many motif finding algorithms, Gibbs sampling is an effective method for long motif finding. In this paper we present an improved Gibbs sampling method on graphics processing units (GPU) to accelerate motif finding. Experimental data support that, compared to traditional programs on CPU, our program running on GPU provides an effective and low cost solution for motif finding problem, especially for long motif finding.
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