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RNA Editing pp 13-34 | Cite as

Computational Detection of Plant RNA Editing Events

  • Alejandro A. EderaEmail author
  • M. Virginia Sanchez-Puerta
Protocol
  • 88 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2181)

Abstract

Computers are able to systematically exploit RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecting RNA editing sites in plant organelles. This framework comprises three major steps: RNA-seq data processing, RNA read alignment, and RNA editing site detection. Each step is discussed in sufficient detail to be implemented by the reader. As a study case, the framework will be used with publicly available sequencing data to detect C-to-U RNA editing sites in the coding sequences of the mitochondrial genome of Nicotiana tabacum.

Key words

RNA editing Land plant RNA sequencing Mitochondrial genome RNA read alignment Nicotiana tabacum 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  • Alejandro A. Edera
    • 1
    Email author
  • M. Virginia Sanchez-Puerta
    • 1
    • 2
  1. 1.Facultad de Ciencias AgrariasIBAM, Universidad Nacional de Cuyo, CONICETAlmirante BrownArgentina
  2. 2.Facultad de Ciencias Exactas y NaturalesUniversidad Nacional de CuyoMendozaArgentina

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