MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Open accessAbstract
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.
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“FASTQ files from BGI Tech Solutions were analysed using the EDGE Bioinformatics web-based platform which uses automated scripts of QIIME2 version 2023.5.1 (Bokulich et al., 2018; Bolyen et al., 2019; Katoh et al., 2002; Li et al., 2017; Price et al., 2009; Rognes et al., 2016).”
InfluentialRevisiting Aurochs Haplogroup C: Paleogenomic Perspectives from Northeastern China
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- Authors
- Katoh, K.
- Affiliations
- Kyoto University (JP)
- Corresponding author
- Katoh, K.
- ORCID
- Katoh, K.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-07-15
- Volume
- 30
- Issue
- 14
- Pages
- 3059-3066
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC135756
- OpenAlex
- W2127774996
- Semantic Scholar
- 63116ca22d65d15a178091ed5b20d89482d7b3db
- Cited by
- 17,027
- References
- 42
- Citations by year
- 2026: 1272 · 2025: 1608 · 2024: 1656 · 2023: 1523 · 2022: 1611 · 2021: 1525 · 2020: 1249 · 2019: 918 · 2018: 836 · 2017: 751 · 2016: 649 · 2015: 619 · 2014: 589 · 2013: 549 · 2012: 471
- FWCI
- 12.43
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- MAFFT, multiple sequence alignment, fast Fourier transform, homology detection, progressive alignment, iterative refinement, CPU time reduction, indels
- MeSH terms
- Computer Simulation, DNA-Directed RNA Polymerases, RNA, Ribosomal, Software, Reproducibility of Results, Sequence Alignment, Spectroscopy, Fourier Transform Infrared
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