Bioinformatics for DNA Sequence Analysis

Volume 537 of the series Methods in Molecular Biology pp 39-64


Multiple Alignment of DNA Sequences with MAFFT

  • Kazutaka KatohAffiliated withDigital Medicine Initiative, Kyushu University
  • , George AsimenosAffiliated withDepartment of Computer Science, Stanford University
  • , Hiroyuki TohAffiliated withMedical Institute of Bioregulation, Kyushu University

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Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.

Key words

Multiple sequence alignment progressive method iterative refinement method consistency objective function genome comparison