Nucleic Acids Research, 2002, Vol. 30, No. 14 3059-3066
© 2002 Oxford University Press
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan and 1 Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
*To whom correspondence should be addressed. Tel: +81 75 753 4220; Fax: +81 75 753 4223; Email: miyata@biophys.kyoto-u.ac.jp
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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S. Deshmukh, R. Huckelhoven, P. Schafer, J. Imani, M. Sharma, M. Weiss, F. Waller, and K.-H. Kogel Colloquium Paper: The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley PNAS, December 5, 2006; 103(49): 18450 - 18457. [Abstract] [Full Text] [PDF]
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F. Oberwinkler, R. Kirschner, F. Arenal, M. Villarreal, V. Rubio, D. Begerow, and R. Bauer Two new pycnidial members of the Atractiellales: Basidiopycnis hyalina and Proceropycnis pinicola. Mycologia, July 1, 2006; 98(4): 637 - 649. [Abstract] [Full Text] [PDF]
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A. Biegert, C. Mayer, M. Remmert, J. Soding, and A. N. Lupas The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W335 - W339. [Abstract] [Full Text] [PDF]
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I. M. Wallace, O. O'Sullivan, D. G. Higgins, and C. Notredame M-Coffee: combining multiple sequence alignment methods with T-Coffee Nucleic Acids Res., March 23, 2006; 34(6): 1692 - 1699. [Abstract] [Full Text] [PDF]
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 A. Schulze Phylogeny and genetic diversity of palolo worms (palola, eunicidae) from the tropical north pacific and the Caribbean. Biol. Bull., February 1, 2006; 210(1): 25 - 37. [Abstract] [Full Text] [PDF]
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S. Chakrabarti, C. J. Lanczycki, A. R. Panchenko, T. M. Przytycka, P. A. Thiessen, and S. H. Bryant Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res., January 1, 2006; 34(9): 2598 - 2606. [Abstract] [Full Text] [PDF]
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M. Gryzenhout, H. Myburg, C. S. Hodges, B. D. Wingfield, and M. J. Wingfield Microthia, Holocryphia and Ursicollum, three new genera on Eucalyptus and Coccoloba for fungi previously known as Cryphonectria. Stud Mycol, January 1, 2006; 55: 35 - 52. [Abstract] [Full Text] [PDF]
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G. Nakabonge, M. Gryzenhout, J. Roux, B. D. Wingfield, and M. J. Wingfield Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa. Stud Mycol, January 1, 2006; 55: 255 - 267. [Abstract] [Full Text] [PDF]
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X. Zhou, Z. W. de Beer, and M. J. Wingfield DNA sequence comparisons of Ophiostoma spp., including Ophiostoma aurorae sp. nov., associated with pine bark beetles in South Africa. Stud Mycol, January 1, 2006; 55: 269 - 277. [Abstract] [Full Text] [PDF]
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Z. W. de Beer, D. Begerow, R. Bauer, G. S. Pegg, P. W. Crous, and M. J. Wingfield Phylogeny of the Quambalariaceae fam. nov., including important Eucalyptus pathogens in South Africa and Australia. Stud Mycol, January 1, 2006; 55: 289 - 298. [Abstract] [Full Text] [PDF]
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S. Hartmann, D. Lu, J. Phillips, and T. J. Vision Phytome: a platform for plant comparative genomics Nucleic Acids Res., January 1, 2006; 34(suppl_1): D724 - D730. [Abstract] [Full Text] [PDF]
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T. Lassmann and E. L. L. Sonnhammer Automatic assessment of alignment quality Nucleic Acids Res., December 16, 2005; 33(22): 7120 - 7128. [Abstract] [Full Text] [PDF]
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A. Pavlicek, R. House, A. J. Gentles, J. Jurka, and B. E. Morrow Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome Genome Res., November 1, 2005; 15(11): 1487 - 1495. [Abstract] [Full Text] [PDF]
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D. G. Higgins, G. Blackshields, and I. M. Wallace Mind the gaps: Progress in progressive alignment PNAS, July 26, 2005; 102(30): 10411 - 10412. [Full Text] [PDF]
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A. Loytynoja and N. Goldman From The Cover: An algorithm for progressive multiple alignment of sequences with insertions PNAS, July 26, 2005; 102(30): 10557 - 10562. [Abstract] [Full Text] [PDF]
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