CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search.

ABSTRACT:

Background

The maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel processing capabilities of modern GPUs with close-to-peak performance. This motivates the need for more efficient implementations.

Results

CUDASW++4.0 is a fast software tool for scanning protein sequence databases with the Smith-Waterman algorithm on CUDA-enabled GPUs. Our approach achieves high efficiency for dynamic programming-based alignment computation by minimizing memory accesses and instructions. We provide both efficient matrix tiling, and sequenc

SUBMITTER: Schmidt B 

PROVIDER: S-EPMC11531700 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature