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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.

    Source

    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
    [PubMed - indexed for MEDLINE]

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