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Plant Transposable Elements pp 69–74Cite as

Mining of Miniature Transposable Elements in Brassica Species at BrassicaTED

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

Abstract

Miniature form transposable elements (mTEs) are ubiquitous in plant genomes and directly linked to gene regulation and evolution. With the advantage of completely sequenced genomes of Brassica rapa and Brassica oleracea, an open-source web portal called, BrassicaTED was developed. This database provides a user-friendly interface to explore invaluable information of mTEs in Brassica species and unique visualization and comparison tools. In this chapter, we describe an overview of this database construction and explain the utilities of data search, visualization, and analysis tools. In addition, we show the possible obstacles users may encounter when using this database.

Key words

  • Brassica
  • Miniature inverted-repeat transposable element (MITE)
  • Terminal-repeat retrotransposon in miniature (TRIM)
  • Miniature form Transposable Elements (mTEs)
  • K BLAST

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Authors and Affiliations

  1. Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea

    Murukarthick Jayakodi & Tae-Jin Yang

Authors
  1. Murukarthick Jayakodi
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  2. Tae-Jin Yang
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Corresponding author

Correspondence to Tae-Jin Yang .

Editor information

Editors and Affiliations

  1. CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai, China

    Dr. Jungnam Cho

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Jayakodi, M., Yang, TJ. (2021). Mining of Miniature Transposable Elements in Brassica Species at BrassicaTED. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_5

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1133-3

  • Online ISBN: 978-1-0716-1134-0

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