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Scanning protein sequence databanks using a distributed processing workstation network.

G J Barton1

  • 1Laboratory of Molecular Biophysics, Oxford, UK.

Computer Applications in the Biosciences : CABIOS
|January 1, 1991
PubMed
Summary
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The pscan program speeds up protein databank scans by distributing the workload across multiple computers. This parallel processing significantly reduces computation time for sequence comparison tasks.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein databank scanning is crucial for sequence comparison and analysis.
  • Conventional methods can be time-consuming, limiting large-scale studies.
  • Parallel processing offers a solution for accelerating computational tasks.

Purpose of the Study:

  • To introduce pscan, a novel program for distributed protein databank scanning.
  • To demonstrate the efficiency of pscan in accelerating sequence comparison.
  • To provide a cost-effective parallel processing alternative.

Main Methods:

  • Developed the pscan program for network-based distributed computing.
  • Integrated pscan with conventional sequence comparison programs.

Related Experiment Videos

  • Utilized the Smith-Waterman dynamic programming algorithm for testing.

    • Main Results:

    • pscan effectively distributes protein databank scans across a network.
    • Tested on a 6858-sequence databank with a 740-residue query.
    • Reduced scan time from approximately 50 minutes (single processor) to 11 minutes (five processors).

    Conclusions:

    • pscan significantly accelerates protein databank scanning through parallel processing.
    • The program offers a low-cost, portable solution compared to dedicated hardware.
    • pscan is compatible with existing sequence comparison tools with minor modifications.