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Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use.

Istvan Ladunga1

  • 1Departments of Statistics, Biochemistry, and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska.

Current Protocols in Bioinformatics
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Summary
This summary is machine-generated.

Researchers can now install the Basic Local Alignment Search Tool (BLAST) locally for high-throughput genomic analysis. This guide provides installation instructions for various operating systems and database management strategies.

Keywords:
BLASTLINUXbiosequence analysissequence similarity search

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Basic Local Alignment Search Tool (BLAST) is a fundamental tool for analyzing novel amino acid and nucleic acid sequences.
  • BLAST is crucial in fields like genomics, transcriptomics, and protein science.
  • Existing BLAST Web servers and cloud resources often do not meet the high-throughput demands or policy requirements of academic and commercial researchers.

Purpose of the Study:

  • To provide a comprehensive guide for the local installation of BLAST.
  • To address the limitations of cloud-based and web server BLAST resources for specific research needs.
  • To enable researchers to perform high-throughput comparative genomic analyses on their own infrastructure.

Main Methods:

  • Detailed instructions for installing BLAST on standalone workstations and compute clusters.
  • Guidance on planning and executing the installation across LINUX, Windows, and Mac OS X operating systems.
  • Strategies for downloading pre-existing and creating custom sequence databases in BLAST format.

Main Results:

  • Successful local installation of BLAST on diverse operating systems.
  • Establishment of local BLAST databases for efficient sequence searching.
  • Facilitation of high-throughput comparative genomic pipelines independent of external servers.

Conclusions:

  • Local BLAST installation is a viable and often necessary solution for researchers with high-throughput or specific policy requirements.
  • This guide empowers researchers to manage their own BLAST resources for advanced genomic analyses.
  • Implementing local BLAST enhances data security and computational control for scientific research.