Published online 20 January 2005
Article |
MAFFT version 5: improvement in accuracy of multiple sequence alignment
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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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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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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 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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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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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. [Abstract] [Full Text] [PDF]
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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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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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