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Related Experiment Videos

Parallelized multiple alignment.

Jens Kleinjung1, Nigel Douglas, Jaap Heringa

  • 1Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.

Bioinformatics (Oxford, England)
|September 10, 2002
PubMed
Summary
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Parallel processing significantly speeds up multiple sequence alignment. The Praline program, enhanced with Message Passing Interface (MPI) routines, achieved up to a tenfold performance increase on 25 processors.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment is crucial for understanding sequence relationships.
  • Large-scale alignments present significant computational challenges.
  • Efficient algorithms are needed to reduce processing time.

Purpose of the Study:

  • To enhance the Praline multiple sequence alignment program with parallel processing capabilities.
  • To reduce the computational cost of generating large sequence alignments.
  • To improve the performance of multiple sequence alignment tools.

Main Methods:

  • Implementation of parallel processing using Message Passing Interface (MPI) routines.
  • Integration of Single Instruction, Multiple Data (SIMD) technology into Praline.

Related Experiment Videos

  • Benchmarking the performance of the parallelized Praline against its single-processor version.

    • Main Results:

    • The parallelized Praline program demonstrated a performance increase of up to ten times.
    • The speedup was observed when utilizing 25 processors for alignment tasks.
    • Computational time for large alignments was considerably reduced.

    Conclusions:

    • Parallel processing effectively addresses the computational expense of multiple sequence alignment.
    • The MPI-enhanced Praline offers a significant speed advantage for large-scale analyses.
    • This approach facilitates more efficient genomic data analysis.