CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.

ABSTRACT:

Background

The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases.

Results

We present CUDASW++ 3.0, a fast Smith-Waterman protein database search algorithm, which couples CPU and GPU SIMD instructions and carries out concurrent CPU and GPU computations. For the CPU computation, this algorithm employs SSE-based vector execution units as accelerators. For the GPU computation, we have investigated for the first time a GPU SIMD parallelization, which employs CUDA PTX SIMD video instructions to gain more data

SUBMITTER: Liu Y 

PROVIDER: S-EPMC3637623 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature