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Related Experiment Videos

Improvement in the accuracy of multiple sequence alignment program MAFFT.

Kazutaka Katoh1, Kei-ichi Kuma, Takashi Miyata

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

Genome Informatics. International Conference on Genome Informatics
|December 20, 2005
PubMed
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The MAFFT multiple sequence alignment program has been enhanced with new iterative refinement options, [GL]-INS-i, significantly improving accuracy for large datasets. These advanced methods offer competitive performance, especially for alignments of 50-100 sequences.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The MAFFT multiple sequence alignment program (v.4 and lower) was fast but less accurate than newer methods like ProbCons and TCoffee v.2.
  • Previous MAFFT versions struggled with accuracy compared to benchmarks released in 2004.

Purpose of the Study:

  • To enhance the accuracy of the MAFFT multiple sequence alignment program with minimal increase in computational cost.
  • Introduce new iterative refinement options to improve alignment quality.

Main Methods:

  • Developed and implemented new iterative refinement options: G-INS-i and L-INS-i ([GL]-INS-i).
  • Introduced a novel objective function combining weighted sum-of-pairs (WSP) score and a COFFEE-like score.
  • Evaluated performance using BAliBASE v.3 (protein) and BRAliBASE (RNA) benchmark datasets.

Related Experiment Videos

Main Results:

  • The [GL]-INS-i options demonstrated improved accuracy, with L-INS-i outperforming other methods on BAliBASE v.3.
  • Accuracy gains were more pronounced for alignments of 50-100 sequences.
  • Explored incorporating homolog information to further boost alignment accuracy.

Conclusions:

  • The enhanced MAFFT (v.5) with [GL]-INS-i options provides highly accurate multiple sequence alignments.
  • [GL]-INS-i options are suitable for up to approximately 200 sequences, balancing accuracy and computational complexity.