Parallel Position Weight Matrices Algorithms

Abstract

Position Weight Matrices (PWMs) are broadly used in computational biology. The basic problem, SCAN, aims to find the occurrences of a given PWM in large 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 and BUCKETSCOREDISTRIBUTION with the CUDA libraries, and report for the different problems speedups of 21x and 77x on a Nvidia GTX 280.