BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization.

ABSTRACT: New High-Performance Computing architectures have been recently developed for commercial central processing unit (CPU). Yet, that has not improved the execution time of widely used bioinformatics applications, like BLAST+. This is due to a lack of optimization between the bases of the existing algorithms and the internals of the hardware that allows taking full advantage of the available CPU cores. To optimize the new architectures, algorithms must be revised and redesigned; usually rewritten from scratch. BLVector adapts the high-level concepts of BLAST+ to the x86 architectures with AVX-512, to harness their capabilities. A deep comprehensive study has been carried out to optimize the approach, with a significant reduction in time execution. BLVector reduces the execution time of BLAST+

SUBMITTER: Galvez S 

PROVIDER: S-EPMC7884812 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature