Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021:2284:253-270.
doi: 10.1007/978-1-0716-1307-8_14.

RNA Editing Detection in HPC Infrastructures

Claudio Lo Giudice  1 , Luigi Mansi  1 , Tiziano Flati  2 , Silvia Gioiosa  2 , Giovanni Chillemi  2   3 , Pietro Libro  4 , Tiziana Castrignanò  4 , Graziano Pesole  1   5   6 , Ernesto Picardi  7   8   9
Affiliations

RNA Editing Detection in HPC Infrastructures

Claudio Lo Giudice et al. Methods Mol Biol. 2021.

Erratum in

  • Correction to: RNA Bioinformatics.
    Picardi E. Picardi E. Methods Mol Biol. 2021;2284:C1. doi: 10.1007/978-1-0716-1307-8_32. Methods Mol Biol. 2021. PMID: 34339024 No abstract available.

Abstract

RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, the detection of RNA editing variants in large transcriptome sequencing experiments (RNAseq) is yet a challenging computational task. To drastically reduce computing times we have developed a novel REDItools version able to identify A-to-I events in huge amount of RNAseq data employing High Performance Computing (HPC) infrastructures.Here we show how to use REDItools v2 in HPC systems.

Keywords: A-to-I editing; Bioinformatics; DNAseq; Deep sequencing; Genomics; HPC; MPI; RNA editing; RNAseq; Transcriptomics.

PubMed Disclaimer

References

    1. Gott JM, Emeson RB (2000) Functions and mechanisms of RNA editing. Annu Rev Genet 34:499–531. https://doi.org/10.1146/annurev.genet.34.1.499 - DOI - PubMed
    1. Bar-Yaacov D, Pilpel Y, Dahan O (2018) RNA editing in bacteria: occurrence, regulation and significance. RNA Biol 15:863–867. https://doi.org/10.1080/15476286.2018.1481698 - DOI - PubMed - PMC
    1. Porath HT, Knisbacher BA, Eisenberg E, Levanon EY (2017) Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance. Genome Biol 18:185. https://doi.org/10.1186/s13059-017-1315-y - DOI - PubMed - PMC
    1. Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A (2013) RNA editing in plants and its evolution. Annu Rev Genet 47:335–352. https://doi.org/10.1146/annurev-genet-111212-133519 - DOI - PubMed
    1. Pfaller CK, Donohue RC, Nersisyan S, Brodsky L, Cattaneo R (2018) Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1p150. PLoS Biol 16:e2006577. https://doi.org/10.1371/journal.pbio.2006577 - DOI - PubMed - PMC

Publication types

LinkOut - more resources