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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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