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Computational Analysis of Transposable Elements and CircRNAs in Plants

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Plant Circular RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2362))

Abstract

This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features. Finally, we investigate the association on circRNAs:TE in plants in the model organism Arabidopsis thaliana.

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Authors and Affiliations

  1. Department of Computer Science, Federal University of Technology—Paraná (UTFPR), Cornélio Procópio, PR, Brazil

    Liliane Santana Oliveira, Andressa Caroline Patera, Douglas Silva Domingues, Danilo Sipoli Sanches, Fabricio Martins Lopes, Pedro Henrique Bugatti, Priscila Tiemi Maeda Saito & Alexandre Rossi Paschoal

  2. Embrapa Soja, Londrina, Paraná, Brazil

    Liliane Santana Oliveira

  3. Group of Genomics and Transcriptomes in Plants, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil

    Douglas Silva Domingues

  4. Centro de Modelamiento Molecular, Biofísica y Bioinformática—CM2B2, Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago, Chile

    Vinicius Maracaja-Coutinho

  5. Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), Cidade Universitária, SP, Brazil

    Alan Mitchell Durham

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  1. Liliane Santana Oliveira
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  2. Andressa Caroline Patera
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  3. Douglas Silva Domingues
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  7. Priscila Tiemi Maeda Saito
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  8. Vinicius Maracaja-Coutinho
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  9. Alan Mitchell Durham
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  10. Alexandre Rossi Paschoal
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Corresponding author

Correspondence to Alexandre Rossi Paschoal .

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  1. Oncativo, Argentina

    Luis María Vaschetto

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Oliveira, L.S. et al. (2021). Computational Analysis of Transposable Elements and CircRNAs in Plants. In: Vaschetto, L.M. (eds) Plant Circular RNAs. Methods in Molecular Biology, vol 2362. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1645-1_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1645-1_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1644-4

  • Online ISBN: 978-1-0716-1645-1

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