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Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.

Multiple alignment of DNA sequences with MAFFT.

Author information

1
Digital Medicine Initiative, Kyushu University, Fukuoka, Japan.

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.

PMID:
19378139
DOI:
10.1007/978-1-59745-251-9_3
[Indexed for MEDLINE]

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