articleNucleic Acids ResearchJul 15, 2002BRONZE OA

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

KKKazutaka Katoh

Kyoto University

PubMed
Indexed incrossrefdoajpubmed

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…

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Topics & keywords

Topics
Keywords
  • Fast Fourier transform
  • Computer science
  • Multiple sequence alignment
  • Split-radix FFT algorithm
  • Sequence (biology)
  • Parallel computing
  • Benchmark (surveying)
  • Algorithm
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