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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Katoh, Kazutaka ; Misawa, Kazuharu ; Kuma, Kei‐ichi ; Miyata, Takashi

Nucleic acids research, 2002-07, Vol.30 (14), p.3059-3066 [Periódico revisado por pares]

England: Oxford University Press

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  • Título:
    MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
  • Autor: Katoh, Kazutaka ; Misawa, Kazuharu ; Kuma, Kei‐ichi ; Miyata, Takashi
  • Assuntos: Computer Simulation ; DNA-Directed RNA Polymerases - genetics ; Reproducibility of Results ; RNA, Ribosomal - genetics ; Sequence Alignment - methods ; Software ; Spectroscopy, Fourier Transform Infrared - methods
  • É parte de: Nucleic acids research, 2002-07, Vol.30 (14), p.3059-3066
  • Notas: To whom correspondence should be addressed. Tel: +81 75 753 4220; Fax: +81 75 753 4223; Email: miyata@biophys.kyoto‐u.ac.jp
    local:gkf436
    ark:/67375/HXZ-NRP1F2B9-4
    istex:5EA93CBE48016E67AE51670E4623847EAB8A8265
    Received April 8, 2002; Revised and Accepted May 24, 2002
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    To whom correspondence should be addressed. Tel: +81 75 753 4220; Fax: +81 75 753 4223; Email: miyata@biophys.kyoto-u.ac.jp
  • Descrição: A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over 100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
  • Editor: England: Oxford University Press
  • Idioma: Inglês
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