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Detection of Transposition Events from Next-Generation Sequencing Data

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

Abstract

Detection of transposition events of a transposon from short reads of next-generation sequencing (NGS) is challenging because transposons are repetitive and difficult to be distinguished from already existing transposons in the genome. Many transposons generate target site duplication (TSD) as the result of chromosomal integration. Since TSDs flanking the 5′-end (head) and 3′-end (tail) of a transposon has the identical sequences which are absent from the reference copy, the short reads containing the head or tail sequences of the transposon following the same TSD sequence may reveal the evidence of transposition. Transposon Insertion Finder (TIF) focuses on the TSD with flanking sequence of transposon and detects transposition events from NGS data. TIF software is available at https://github.com/akiomiyao/tif.

Key words

  • Transposable elements
  • Retroelements
  • Bioinformatics
  • Sequence analysis

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Correspondence to Akio Miyao .

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Miyao, A. (2021). Detection of Transposition Events from Next-Generation Sequencing Data. 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_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_12

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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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