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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Robert C Edgar1

  • 1bob@drive5.com

Nucleic Acids Research
|March 23, 2004
PubMed
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We introduce MUSCLE, a new protein sequence alignment program. MUSCLE offers high accuracy and speed, outperforming other methods on benchmark tests for biological sequence analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Multiple sequence alignment is crucial for understanding protein evolution and function.
  • Existing alignment tools face challenges with speed and accuracy, especially for large datasets.

Purpose of the Study:

  • To introduce MUSCLE, a novel computer program for protein sequence multiple alignment.
  • To evaluate MUSCLE's performance against established alignment software.

Main Methods:

  • MUSCLE utilizes kmer counting for fast distance estimation.
  • Progressive alignment is enhanced with a log-expectation score profile function.
  • Tree-dependent restricted partitioning is employed for refinement.

Main Results:

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  • MUSCLE demonstrated top-tier accuracy across multiple benchmark datasets (BAliBASE, SABmark, SMART, PREFAB).
  • The program is significantly faster than other methods for large-scale alignments.
  • Unrefined MUSCLE shows accuracy comparable to T-Coffee and MAFFT.

Conclusions:

  • MUSCLE is an accurate and efficient tool for multiple protein sequence alignment.
  • Its speed makes it suitable for analyzing large biological sequence datasets.
  • The MUSCLE program and associated data are publicly available for research use.