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A platform for biological sequence comparison on parallel computers.

A S Deshpande1, D S Richards, W R Pearson

  • 1Department of Computer Science, University of Virginia, Charlottesville 22908.

Computer Applications in the Biosciences : CABIOS
|April 1, 1991
PubMed
Summary
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Two new programs, PSCANLIB and PCOMPLIB, accelerate biological sequence database searches on Intel hypercube computers using FASTA and Smith-Waterman algorithms.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Biological sequence database searching is computationally intensive.
  • Efficient algorithms are crucial for analyzing large biological datasets.

Purpose of the Study:

  • To develop and implement parallelized programs for rapid biological sequence similarity searching.
  • To provide a flexible framework for integrating different sequence comparison algorithms.

Main Methods:

  • Development of two programs: PSCANLIB (single sequence vs. library) and PCOMPLIB (library vs. library).
  • Implementation on Intel hypercube computers utilizing parallel processing.
  • Integration of the FASTA and Smith-Waterman sequence comparison algorithms.

Related Experiment Videos

Main Results:

  • PSCANLIB achieved a 229-amino acid protein sequence search against a 3.4 million residue library in 16 seconds using FASTA.
  • The same search with Smith-Waterman algorithm took 35 minutes.
  • PCOMPLIB compared a 0.8 million amino acid library against itself in 5.3 minutes using FASTA on a 32-node hypercube.

Conclusions:

  • The developed programs significantly accelerate biological sequence similarity searches.
  • The parallelized approach on hypercube computers offers a scalable solution for large-scale bioinformatics analyses.
  • The framework allows for easy integration of alternative search algorithms for future applications.