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Article Dans Une Revue Parallel Computing Année : 2011

Parallel Position Weight Matrices Algorithms

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Position Weight Matrices (PWMs) are broadly used in computational biology. The basic problems, Scan and MultipleScan, aim to find all the occurrences of a given PWM or a set of PWMs in long sequences. Some other PWM tasks share a common NP-hard subproblem, ScoreDistribution. The existing algorithms rely on the enumeration on a large set of scores or words, and they are mostly not suitable for parallelization. We propose a new algorithm, BucketScoreDistribution, that is both very efficient and suitable for parallelization. We bound the error induced by this algorithm. We realized a GPU prototype for Scan, MultipleScan and BucketScoreDistribution with the CUDA libraries, and report for the different problems speedups larger than 10× on several Nvidia cards.
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hal-00623404 , version 1 (14-09-2011)



Mathieu Giraud, Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. Parallel Computing, 2011, 37, pp.466-478. ⟨10.1016/j.parco.2010.10.001⟩. ⟨hal-00623404⟩
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