RT Journal Article
T1 BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
A1 Gálvez-Rojas, Sergio
A1 Federico, Agostini
A1 Caselli, Javier
A1 Hernández, Pilar
A1 Dorado, Gabriel
K1 Hardware
K1 Arquitectura de ordenadores
AB 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+ when aligning up to mid-size protein sequences (∼750 amino acids). The gain in real scenario cases is 3.2-fold. When applied to longer proteins, BLVector consumes more time than BLAST+, but retrieves a much larger set of results. BLVector and BLAST+ are fine-tuned heuristics. Therefore, the relevant results returned by both are the same, although they behave differently specially when performing alignments with low scores. Hence, they can be considered complementary bioinformatics tools.
PB Frontiers
YR 2021
FD 2021-02-02
LK https://hdl.handle.net/10630/35713
UL https://hdl.handle.net/10630/35713
LA eng
NO Gálvez S, Agostini F, Caselli J, Hernandez P and Dorado G (2021) BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization. Front. Genet. 12:618659. doi: 10.3389/fgene.2021.618659
NO This work was supported by the Ministerio de Ciencia e Innovación (MINECO grants BIO2015-64737-R, PID2019-109089RB-C32, and PID2019-108195GB-I00), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (MINECO and INIA RF2012-00002-C02-02), Consejería de Agricultura y Pesca (041/C/2007, 75/C/2009, and 56/C/2010), Consejería de Economía, Innovación y Ciencia (P18-RT-992 and P11-AGR-7322), Grupo PAI (AGR-248) of Junta de Andalucía, and Universidad de Córdoba (Ayuda a Grupos), Spain.
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 21 ene 2026