Published online 20 January 2005
Article |
MAFFT version 5: improvement in accuracy of multiple sequence alignment
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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J. Pei, B.-H. Kim, and N. V. Grishin PROMALS3D: a tool for multiple protein sequence and structure alignments Nucleic Acids Res., April 1, 2008; 36(7): 2295 - 2300. [Abstract] [Full Text] [PDF]
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K. M. Bushell, C. Sollner, B. Schuster-Boeckler, A. Bateman, and G. J. Wright Large-scale screening for novel low-affinity extracellular protein interactions Genome Res., April 1, 2008; 18(4): 622 - 630. [Abstract] [Full Text] [PDF]
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J. D. Moore and R. G. Allaby TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism Bioinformatics, March 1, 2008; 24(5): 717 - 718. [Abstract] [Full Text] [PDF]
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W. Pirovano, K. A. Feenstra, and J. Heringa PRALINETM: a strategy for improved multiple alignment of transmembrane proteins Bioinformatics, February 15, 2008; 24(4): 492 - 497. [Abstract] [Full Text] [PDF]
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S. Michael, G. Trave, C. Ramu, C. Chica, and T. J. Gibson Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation Bioinformatics, February 15, 2008; 24(4): 453 - 457. [Abstract] [Full Text] [PDF]
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M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Perin GreenPhylDB: a database for plant comparative genomics Nucleic Acids Res., January 11, 2008; 36(suppl_1): D991 - D998. [Abstract] [Full Text] [PDF]
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C. Casola, D. Hucks, and C. Feschotte Convergent Domestication of pogo-like Transposases into Centromere-Binding Proteins in Fission Yeast and Mammals Mol. Biol. Evol., January 1, 2008; 25(1): 29 - 41. [Abstract] [Full Text] [PDF]
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S. Wang, R. R. Gutell, and D. P. Miranker Biclustering as a method for RNA local multiple sequence alignment Bioinformatics, December 15, 2007; 23(24): 3289 - 3296. [Abstract] [Full Text] [PDF]
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P. A. Watkins, D. Maiguel, Z. Jia, and J. Pevsner Evidence for 26 distinct acyl-coenzyme A synthetase genes in the human genome J. Lipid Res., December 1, 2007; 48(12): 2736 - 2750. [Abstract] [Full Text] [PDF]
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T. Schlegel, O. Mirus, A. von Haeseler, and E. Schleiff The Tetratricopeptide Repeats of Receptors Involved in Protein Translocation across Membranes Mol. Biol. Evol., December 1, 2007; 24(12): 2763 - 2774. [Abstract] [Full Text] [PDF]
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T. Golubchik, M. J. Wise, S. Easteal, and L. S. Jermiin Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments Mol. Biol. Evol., November 1, 2007; 24(11): 2433 - 2442. [Abstract] [Full Text] [PDF]
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