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Plant Transposable Elements pp 111–114Cite as

Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq

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

Abstract

ALE-seq is a method devised to identify pre-integration intermediates of LTR retrotransposons called extrachromosomal linear DNA, which can be used to predict retrotransposition activity. We describe here a bioinformatic methodology to process reads obtained from the ALE-seq protocol for the effective annotation of novel and active retroelements.

Key words

  • LTR retrotransposon
  • Extrachromosomal DNA
  • ALE-seq

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  • DOI: 10.1007/978-1-0716-1134-0_10
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References

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Acknowledgments

This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB27030209) and the National Natural Science Foundation of China (31970518) granted to J.C.

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Authors and Affiliations

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

    Ling Wang, Jungnam Cho & Viswanathan Satheesh

  2. CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China

    Jungnam Cho

Authors
  1. Ling Wang
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  2. Jungnam Cho
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  3. Viswanathan Satheesh
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Corresponding author

Correspondence to Viswanathan Satheesh .

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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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Wang, L., Cho, J., Satheesh, V. (2021). Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq. 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_10

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_10

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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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