Position Weight Matrices (PWMs) are broadly used in computation biology. The basic problem, Scan, aims to find the occurrences of a given PWM in large sequences. A number of other PWMs tasks share a common subproblem, ScoreDistribution, that has been shown to be NP-hard. 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.