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Related Experiment Videos

A parallel computing approach to genetic sequence comparison: the master-worker paradigm with interworker

D F Sittig1, D Foulser, N Carriero

  • 1Department of Anesthesiology, Yale University, New Haven, Connecticut 06510.

Computers and Biomedical Research, an International Journal
|April 1, 1991
PubMed
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We developed a parallel genetic sequence comparison algorithm using C-Linda on multiple processors. This approach significantly speeds up biological sequence analysis by efficiently comparing genetic data.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Parallel Computing

Background:

  • Genetic sequence comparison is crucial for understanding biological functions.
  • Traditional sequential algorithms can be computationally intensive.
  • Parallel computing offers potential for accelerating these analyses.

Purpose of the Study:

  • To evaluate the applicability of parallel computers for genetic sequence comparisons.
  • To implement and test a parallel dynamic programming algorithm.
  • To assess performance improvements over sequential methods.

Main Methods:

  • Implemented a master-worker (MW) parallel algorithm using C-Linda.
  • Utilized a shared associative memory model (tuple space) for process communication.

Related Experiment Videos

  • Tested on Sequent Symmetry and Intel Hypercube parallel systems.
  • Incorporated global interworker communication to optimize search time.

    • Main Results:

    • Demonstrated successful implementation of a parallel genetic sequence comparison algorithm.
    • Achieved performance gains through parallelization on different hardware architectures.
    • The global abort threshold method effectively reduced total search time.

    Conclusions:

    • Parallel computing, specifically with C-Linda, is a viable approach for accelerating genetic sequence comparisons.
    • The MW implementation with global communication offers significant speedup.
    • This work highlights the potential of parallel algorithms in bioinformatics.