173
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Recent developments in the MAFFT multiple sequence alignment program.

      1 ,
      Briefings in bioinformatics
      Oxford University Press (OUP)

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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/.

          Related collections

          Author and article information

          Journal
          Brief Bioinform
          Briefings in bioinformatics
          Oxford University Press (OUP)
          1477-4054
          1467-5463
          Jul 2008
          : 9
          : 4
          Affiliations
          [1 ] Digital Medicine Initiative, Kyushu University, Fukuoka 812-8582, Japan. katoh@bioreg.kyushu-u.ac.jp
          Article
          bbn013
          10.1093/bib/bbn013
          18372315
          9f1d45ae-3e8e-4d36-a322-042586c4d8fc
          History

          Comments

          Comment on this article