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Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments.

Won Cheol Yim1, John C Cushman1

  • 1Department of Biochemistry and Molecular Biology, University of Nevada-Reno, Reno, NV, United States of America.

Peerj
|June 28, 2017
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Summary

Divide and Conquer BLAST (DCBLAST) accelerates sequence similarity searches on high-performance computing (HPC) systems. This tool simplifies parallel processing for large datasets, significantly reducing computation time for bioinformatics tasks.

Keywords:
BLASTDistributed computingEnvironmentHPCParallel processingSequence similarity

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Large-scale biological datasets pose computational challenges, particularly for sequence similarity searches.
  • The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) is widely used but CPU-intensive.
  • Existing parallel solutions for sequence analysis often require advanced computational expertise.

Purpose of the Study:

  • To develop a user-friendly, parallel approach for accelerating NCBI BLAST searches.
  • To enable efficient sequence similarity searches in distributed computing environments like clusters, grids, and HPC systems.
  • To overcome the speed limitations of single-node BLAST programs for large-scale data analysis.

Main Methods:

  • Development of Divide and Conquer BLAST (DCBLAST) software.
  • Implementation of a query sequence distribution strategy for parallel processing.
  • Testing and validation of DCBLAST on high-performance computing (HPC) systems.

Main Results:

  • DCBLAST significantly improves processing speed when scaling from one to 256 CPU cores.
  • The tool demonstrates robust performance across multiple nodes automatically.
  • DCBLAST overcomes single-node speed limitations and has no output restrictions.

Conclusions:

  • DCBLAST offers a simple, accessible, and robust parallel solution for accelerating BLAST searches.
  • The tool facilitates rapid discovery of sequence similarities in very large datasets.
  • DCBLAST simplifies distributed computation pipelines for bioinformatics researchers.