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

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 algor...

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Autores principales: Gálvez, Sergio, Agostini, Federico, Caselli, Javier, Hernandez, Pilar, Dorado, Gabriel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884812/
https://www.ncbi.nlm.nih.gov/pubmed/33603776
http://dx.doi.org/10.3389/fgene.2021.618659
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author Gálvez, Sergio
Agostini, Federico
Caselli, Javier
Hernandez, Pilar
Dorado, Gabriel
author_facet Gálvez, Sergio
Agostini, Federico
Caselli, Javier
Hernandez, Pilar
Dorado, Gabriel
author_sort Gálvez, Sergio
collection PubMed
description 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.
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spelling pubmed-78848122021-02-17 BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization Gálvez, Sergio Agostini, Federico Caselli, Javier Hernandez, Pilar Dorado, Gabriel Front Genet Genetics 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. Frontiers Media S.A. 2021-02-02 /pmc/articles/PMC7884812/ /pubmed/33603776 http://dx.doi.org/10.3389/fgene.2021.618659 Text en Copyright © 2021 Gálvez, Agostini, Caselli, Hernandez and Dorado. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Gálvez, Sergio
Agostini, Federico
Caselli, Javier
Hernandez, Pilar
Dorado, Gabriel
BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title_full BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title_fullStr BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title_full_unstemmed BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title_short BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization
title_sort blvector: fast blast-like algorithm for manycore cpu with vectorization
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884812/
https://www.ncbi.nlm.nih.gov/pubmed/33603776
http://dx.doi.org/10.3389/fgene.2021.618659
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