Blog
About

  • Record: found
  • Abstract: found
  • Article: not found

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

Nucleic Acids Research

DNA-Directed RNA Polymerases, genetics, RNA, Ribosomal, Reproducibility of Results, methods, Sequence Alignment, Software, Spectroscopy, Fourier Transform Infrared, Computer Simulation

Read this article at

ScienceOpenPMC
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      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.

      Related collections

      Author and article information

      Journal
      12136088
      135756

      Comments

      Comment on this article