Computational Analysis of Transposable Elements and CircRNAs in Plants

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...

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Published inMethods in molecular biology (Clifton, N.J.) Vol. 2362; p. 147
Main Authors Oliveira, Liliane Santana, Patera, Andressa Caroline, Domingues, Douglas Silva, Sanches, Danilo Sipoli, Lopes, Fabricio Martins, Bugatti, Pedro Henrique, Saito, Priscila Tiemi Maeda, Maracaja-Coutinho, Vinicius, Durham, Alan Mitchell, Paschoal, Alexandre Rossi
Format Journal Article
LanguageEnglish
Published United States 2021
Subjects
Arabidopsis - genetics
Computational Biology
DNA Transposable Elements - genetics
Plants - genetics
RNA, Circular
Computational methods
Data analysis
Databases
Noncoding
Interaction
Mobile elements
Circular RNA
CircRNAs
Bioinformatics
Transposable elements
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Summary: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.
ISSN:1940-6029
DOI:10.1007/978-1-0716-1645-1_9