Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

ABSTRACT:

Background

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators.

Results

This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level

SUBMITTER: Lan H 

PROVIDER: S-EPMC4959381 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature