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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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Correspondence to Tae-Jin Yang .

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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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