Recent developments in the MAFFT multiple sequence alignment program

The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges...

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Bibliographic Details
Published in:Brief Bioinform Vol. 9; no. 4; pp. 286 - 298
Main Authors: Katoh, Kazutaka, Toh, Hiroyuki
Format: Journal Article
Language:English
Published: England Oxford University Press 01.07.2008
Oxford Publishing Limited (England)
Subjects:
Algorithms
Artificial Intelligence
Bioinformatics
Data analysis
Deoxyribonucleic acid
DNA
Objective function
Pattern Recognition, Automated - methods
Pattern Recognition, Automated - trends
Proteins
Sequence Alignment - methods
Sequence Alignment - trends
Sequence Analysis - methods
Sequence Analysis - trends
Software - trends
Software upgrading
amino acid sequence alignment
ncRNA structural alignment
large-scale sequence alignment
fast tree building
ISSN:1467-5463, 1477-4054, 1477-4054
Online Access:Get full text
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Summary:The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional noncoding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these problems, in 2007, we updated MAFFT to Version 6 with two new techniques: the PartTree algorithm and the Four-way consistency objective function. The former improved the scalability of progressive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/.
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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbn013