title: MAFFT version 5: improvement in accuracy of multiple sequence alignment.
abstract: 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.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan. kkatoh@kuicr.kyoto-u.ac.jp
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Katoh
authors.forename: Kei-ichi
authors.initials: K
authors.lastname: Kuma
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Toh
authors.forename: Takashi
authors.initials: T
authors.lastname: Miyata
mesh_terms: D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017385:Sequence Homology; D012984:Software; D013997:Time Factors