CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions.

ABSTRACT:

Background

Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models.

Findings

This paper describes the latest release of the CUDASW++ software, CUDASW++ 2.0, which makes new contributions to Smith-Waterman protein database searches using compute unified device architecture (CUDA). A parallel Smith-Waterman algorithm is proposed to further opti

SUBMITTER: Liu Y 

PROVIDER: S-EPMC2907862 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature