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

Sergio Gálvez1, Federico Agostini2, Javier Caselli1

  • 1Departamento Lenguajes y Ciencias de la Computación, Universidad de Málaga, Málaga, Spain.

Frontiers in Genetics
|February 19, 2021
PubMed
Summary
This summary is machine-generated.

BLVector optimizes the BLAST+ bioinformatics application for modern CPUs, significantly reducing alignment times for mid-size protein sequences. This tool complements BLAST+ by offering a different approach to sequence alignment, especially for low-score alignments.

Keywords:
benchmarkingdatabase searchpairwise alignmentparallel algorithmproteins

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Modern High-Performance Computing (HPC) architectures, specifically commercial central processing unit (CPU) advancements, have not translated into improved execution times for critical bioinformatics applications such as BLAST+.
  • This performance gap stems from a lack of optimization between existing algorithm designs and the internal hardware capabilities, preventing full utilization of available CPU cores.

Purpose of the Study:

  • To adapt high-level bioinformatics algorithms, specifically BLAST+, to leverage the advanced capabilities of modern x86 architectures with AVX-512 instruction sets.
  • To significantly reduce the execution time of sequence alignment tasks by redesigning and optimizing algorithms for contemporary hardware.

Main Methods:

  • Development of BLVector, a novel approach that translates the core concepts of BLAST+ to be compatible with x86 architectures featuring AVX-512.
  • Conducting a comprehensive study to deeply optimize the BLVector approach for maximum performance gains.

Main Results:

  • BLVector achieves a substantial reduction in execution time for aligning mid-size protein sequences (approximately 750 amino acids), demonstrating a 3.2-fold speedup in real-world scenarios.
  • For longer protein sequences, BLVector may require more time than BLAST+ but yields a significantly larger set of relevant results.
  • Both BLVector and BLAST+ are heuristic tools; while they return similar relevant results, their performance characteristics differ, particularly with low-scoring alignments, positioning them as complementary tools.

Conclusions:

  • BLVector effectively harnesses the power of modern AVX-512 enabled CPUs to accelerate bioinformatics sequence alignment tasks.
  • The tool offers a complementary approach to BLAST+, providing performance benefits for mid-size sequences and a broader result set for longer sequences.
  • The optimization of bioinformatics algorithms for specific hardware architectures is crucial for advancing computational biology research.