Article

MAFFT version 5: Improvement in accuracy of multiple sequence alignment

Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 02/2005; 33(2):511-8. DOI: 10.1093/nar/gki198
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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 ∼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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    • "with coding sequences , the nucleotide alignment was constrained by the amino acid sequences alignment . Although the number of sequences was small in each taxonomic group , we compared the alignments obtained with MUSCLE and submitted the raw amino acid sequences to the GUIDANCE filter ( Penn et al . 2010 ) , using the alignment algorithm MAFFT ( Katoh et al . 2005 ) . MUSCLE and MAFFT produced very similar outputs and we therefore chose the alignments produced by the former ( Additional file 1 : Figure S1 , Additional file 3 : Figure S2 , Additional file 4 : Figure S3 ) . GUIDANCE provided us alignment scores and regions of the align - ments that were not well supported ( Additional file 1 : Figu"
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    • "The alignment of C. temensis mtCR sequences was made with the L-INS-i algorithm of MAFFT (Katoh et al. 2005). Unique haplotypes were confirmed from our previous study with DNAsp (Rozas et al. 2003) (considering gaps as a fifth state), which was also used to calculate molecular diversity at each locality. "
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