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Cited by 4,837

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Open access
Katoh, K.·2005·Nucleic Acids Research
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 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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Metadata

Authors
Katoh, K.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2005-01-19
Volume
33
Issue
2
Pages
511-518
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gki198
OpenAlex
W2102502076
Cited by
4,837
References
2
FWCI
40.45
Type
journal article
Language
en
Open access
gold

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