4.6 Article

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

期刊

FRONTIERS IN GENETICS
卷 12, 期 -, 页码 -

出版社

FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2021.618659

关键词

proteins; parallel algorithm; benchmarking; pairwise alignment; database search

资金

  1. Ministerio de Ciencia e Innovacion (MINECO) [BIO2015-64737-R, PID2019-109089RB-C32, PID2019-108195GB-I00]
  2. Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (MINECO)
  3. Consejeria de Agricultura y Pesca [041/C/2007, 75/C/2009, 56/C/2010]
  4. Consejeria de Economia, Innovacion y Ciencia [P18-RT-992, P11-AGR-7322]
  5. Grupo PAI of Junta de Andalucia [AGR-248]
  6. Universidad de Cordoba (Ayuda a Grupos), Spain
  7. Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) [RF2012-00002-C02-02]

向作者/读者索取更多资源

The development of new high-performance computing architectures has not improved the execution time of widely used bioinformatics applications. Optimization of algorithms is necessary to take full advantage of new hardware, with BLVector showing significant reduction in execution time compared to BLAST+.
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 (similar to 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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