BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs.

ABSTRACT:

Background

The identification of all matches of a large set of position weight matrices (PWMs) in long DNA sequences requires significant computational resources for which a number of efficient yet complex algorithms have been proposed.

Results

We propose BLAMM, a simple and efficient tool inspired by high performance computing techniques. The workload is expressed in terms of matrix-matrix products that are evaluated with high efficiency using optimized BLAS library implementations. The algorithm is easy to parallelize and implement on CPUs and GPUs and has a runtime that is independent of the selected p-value. In terms of single-core performance, it is competitive with state-of-the-art software for PWM matching while being much more efficient when using multithreading. Add

SUBMITTER: Fostier J 

PROVIDER: S-EPMC7068855 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature