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Related Experiment Videos

MAFFT version 5: improvement in accuracy of multiple sequence alignment.

Kazutaka Katoh1, Kei-ichi Kuma, Hiroyuki Toh

  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan. kkatoh@kuicr.kyoto-u.ac.jp

Nucleic Acids Research
|January 22, 2005
PubMed
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The MAFFT multiple sequence alignment program now offers improved accuracy with new iterative refinement options. Aligning sequences with related homologues further enhances accuracy, especially with the new MAFFT features.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding protein and nucleic acid evolution.
  • Existing MSA tools like MAFFT, TCoffee, and CLUSTAL W have varying accuracy levels.
  • Incorporating homologous sequences can potentially improve MSA accuracy.

Purpose of the Study:

  • To introduce and evaluate new iterative refinement options in MAFFT (version 5.3).
  • To compare the accuracy of the new MAFFT options against existing methods.
  • To investigate the impact of including homologous sequences on MSA accuracy.

Main Methods:

  • Implemented new iterative refinement options (H-INS-i, F-INS-i, G-INS-i) in MAFFT 5.3, incorporating pairwise alignment information.

Related Experiment Videos

  • Conducted benchmark tests using alignments of over 50 sequences.
  • Developed a Ruby script (mafftE.rb) to align input sequences with homologous sequences retrieved from SwissProt using NCBI-BLAST.

    • Main Results:

    • The new MAFFT options demonstrated higher accuracy compared to TCoffee v2 and CLUSTAL W in benchmark tests.
    • The new MAFFT options maintain the ability to handle hundreds of sequences on standard hardware.
    • Including dozens of close homologues (E-value < 10^-5 to 10^-20) improved alignment accuracy by 2-10 percentage points, particularly for the new MAFFT options.

    Conclusions:

    • MAFFT version 5.3 offers enhanced accuracy for multiple sequence alignment through new iterative refinement strategies.
    • The inclusion of homologous sequences significantly boosts MSA accuracy, especially when using the advanced MAFFT algorithms.
    • The developed mafftE.rb script provides a practical tool for leveraging homologous sequences to improve alignment quality.