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Nucleic Acids Res. 2005 Jan 20;33(2):511-8. Print 2005.

MAFFT version 5: improvement in accuracy of multiple sequence alignment.

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  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan.


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 approximately 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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