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Related Experiment Videos

MUSCLE: a multiple sequence alignment method with reduced time and space complexity.

Robert C Edgar1

  • 1Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA. bob@drive5.com

BMC Bioinformatics
|August 21, 2004
PubMed
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MUSCLE, a protein sequence alignment program, offers enhanced speed and accuracy. A new variant, MUSCLE-fast, significantly accelerates high-throughput applications while maintaining competitive alignment quality.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Introduced MUSCLE, a novel program for multiple protein sequence alignment.
  • Previous work demonstrated MUSCLE's superior performance on alignment accuracy benchmarks.
  • This paper details previously unpublished algorithmic improvements and introduces MUSCLE-fast for high-throughput applications.

Purpose of the Study:

  • To provide a comprehensive discussion of the MUSCLE algorithm, including new techniques.
  • To introduce and evaluate MUSCLE-fast, a high-speed variant for large-scale applications.
  • To compare the speed and accuracy of MUSCLE variants against existing alignment tools.

Main Methods:

  • Comparative analysis of MUSCLE (default, -fast, -prog variants) against CLUSTALW, Progressive POA, and MAFFT (FFTNS1).

Related Experiment Videos

  • Accuracy assessment using four established benchmarks: BAliBASE, PREFAB, SABmark, and SMART.
  • Performance evaluation on a contemporary desktop computer, measuring alignment time and accuracy.

    • Main Results:

    • MUSCLE-fast demonstrated superior speed across all test datasets, outperforming other methods by two to three orders of magnitude.
    • MUSCLE-fast achieved alignment accuracy comparable to CLUSTALW.
    • The MUSCLE-fast variant aligned 1,000 sequences (average length 282) in 21 seconds.

    Conclusions:

    • MUSCLE provides versatile options for improved speed and/or alignment accuracy.
    • MUSCLE represents a significant advancement over existing protein sequence alignment programs.
    • The MUSCLE software is publicly accessible for research and application.