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Multiple Alignment of DNA Sequences with MAFFT

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Book cover Bioinformatics for DNA Sequence Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 537))

Abstract

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.

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Acknowledgments

We thank Chuong B. Do for critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Digital Medicine Initiative, Kyushu University, 812-8582, Fukuoka, Japan

    Kazutaka Katoh

  2. Department of Computer Science, Stanford University, Stanford, CA, USA

    George Asimenos

  3. Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan

    Hiroyuki Toh

Authors
  1. Kazutaka Katoh
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  2. George Asimenos
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  3. Hiroyuki Toh
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Editor information

Editors and Affiliations

  1. Dept. Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, 36310, Spain

    David Posada

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Katoh, K., Asimenos, G., Toh, H. (2009). Multiple Alignment of DNA Sequences with MAFFT. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_3

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  • DOI: https://doi.org/10.1007/978-1-59745-251-9_3

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-910-9

  • Online ISBN: 978-1-59745-251-9

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