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Nucleic Acids Research 2005 33(2):511-518; doi:10.1093/nar/gki198
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Published online 20 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 2 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


Article

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Kazutaka Katoh1,*, Kei-ichi Kuma1, Hiroyuki Toh1 and Takashi Miyata2,3,4

1 Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan 2 Biohistory Research Hall Takatsuki, Osaka 569-1125, Japan 3 Department of Electrical Engineering and Bioscience, Science and Engineering, Waseda University Tokyo 169-8555, Japan 4 Department of Biophysics, Graduate School of Science, Kyoto University Kyoto 606-8502, Japan

*To whom correspondence should be addressed. Tel: +81 774 38 3119; Fax: +81 774 38 3059; Email: kkatoh{at}kuicr.kyoto-u.ac.jp

Received October 14, 2004. Revised November 16, 2004. Accepted December 29, 2004.

The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of ~8 sequences with low similarity, the accuracy was improved (2–10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10–5–10–20) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.


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Genomic characterization of the first insectivoran papillomavirus reveals an unusually long, second non-coding region and indicates a close relationship to Betapapillomavirus
J. Gen. Virol., March 1, 2009; 90(3): 626 - 633.
[Abstract] [Full Text] [PDF]


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Plant Cell PhysiolHome page
F. del Viso, A. F. Puebla, C. M. Fusari, A. C. Casabuono, A. S. Couto, H. G. Pontis, H. E. Hopp, and R. A. Heinz
Molecular Characterization of a Putative Sucrose:Fructan 6-Fructosyltransferase (6-SFT) of the Cold-Resistant Patagonian Grass Bromus pictus Associated With Fructan Accumulation Under Low Temperatures
Plant Cell Physiol., March 1, 2009; 50(3): 489 - 503.
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Proc R Soc BHome page
J. A Jurado-Rivera, A. P Vogler, C. A.M Reid, E. Petitpierre, and J. Gomez-Zurita
DNA barcoding insect-host plant associations
Proc R Soc B, February 22, 2009; 276(1657): 639 - 648.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
K. M. Eriksson, A. K. Clarke, L.-G. Franzen, M. Kuylenstierna, K. Martinez, and H. Blanck
Community-Level Analysis of psbA Gene Sequences and Irgarol Tolerance in Marine Periphyton
Appl. Envir. Microbiol., February 15, 2009; 75(4): 897 - 906.
[Abstract] [Full Text] [PDF]


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BioinformaticsHome page
M. Hamada, H. Kiryu, K. Sato, T. Mituyama, and K. Asai
Prediction of RNA secondary structure using generalized centroid estimators
Bioinformatics, February 15, 2009; 25(4): 465 - 473.
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Nucleic Acids ResHome page
T. Lassmann, O. Frings, and E. L. L. Sonnhammer
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
Nucleic Acids Res., February 1, 2009; 37(3): 858 - 865.
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Plant Physiol.Home page
O. Wilkins, H. Nahal, J. Foong, N. J. Provart, and M. M. Campbell
Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors
Plant Physiology, February 1, 2009; 149(2): 981 - 993.
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J. Virol.Home page
C. Polacek, J. E. Foley, and E. Harris
Conformational Changes in the Solution Structure of the Dengue Virus 5' End in the Presence and Absence of the 3' Untranslated Region
J. Virol., January 15, 2009; 83(2): 1161 - 1166.
[Abstract] [Full Text] [PDF]


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Genome Biol EvolHome page
Y. Niimura
On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species
Genome Biol Evol, January 1, 2009; 1(0): 34 - 44.
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Genome Biol EvolHome page
D. Dong, G. He, S. Zhang, and Z. Zhang
Evolution of Olfactory Receptor Genes in Primates Dominated by Birth-and-Death Process
Genome Biol Evol, January 1, 2009; 1(0): 258 - 264.
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SIMHome page
K. Tanaka, K. Hirayama, H. Yonezawa, S. Hatakeyama, Y. Harada, T. Sano, T. Shirouzu, and T. Hosoya
Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs.
Stud Mycol, January 1, 2009; 64: 175 - 209.
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GeneticsHome page
F. C. Almeida and R. DeSalle
Orthology, Function and Evolution of Accessory Gland Proteins in the Drosophila repleta Group
Genetics, January 1, 2009; 181(1): 235 - 245.
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Mol Biol EvolHome page
S. Kuraku, A. Meyer, and S. Kuratani
Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?
Mol. Biol. Evol., January 1, 2009; 26(1): 47 - 59.
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Nucleic Acids ResHome page
D. M. A. Martin, D. Miranda-Saavedra, and G. J. Barton
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D244 - D250.
[Abstract] [Full Text] [PDF]


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Mol Biol EvolHome page
M. Kutsukake, N. Nikoh, H. Shibao, C. Rispe, J.-C. Simon, and T. Fukatsu
Evolution of Soldier-Specific Venomous Protease in Social Aphids
Mol. Biol. Evol., December 1, 2008; 25(12): 2627 - 2641.
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Mol Biol EvolHome page
D. Chalkia, N. Nikolaidis, W. Makalowski, J. Klein, and M. Nei
Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments
Mol. Biol. Evol., December 1, 2008; 25(12): 2717 - 2733.
[Abstract] [Full Text] [PDF]


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Appl. Environ. Microbiol.Home page
P. H. Degnan and N. A. Moran
Diverse Phage-Encoded Toxins in a Protective Insect Endosymbiont
Appl. Envir. Microbiol., November 1, 2008; 74(21): 6782 - 6791.
[Abstract] [Full Text] [PDF]



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