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Benchmarking RNA Editing Detection Tools
RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identif...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10527054/ https://www.ncbi.nlm.nih.gov/pubmed/37754200 http://dx.doi.org/10.3390/biotech12030056 |
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author | Morales, David Rodríguez Rennie, Sarah Uchida, Shizuka |
author_facet | Morales, David Rodríguez Rennie, Sarah Uchida, Shizuka |
author_sort | Morales, David Rodríguez |
collection | PubMed |
description | RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identified: (1) the most frequent, adenosine to inosine (A-to-I); and (2) the less frequent, cysteine to uracil (C-to-U) RNA editing. Unlike other epitranscriptomic marks, RNA editing can be readily detected from RNA sequencing (RNA-seq) data without any chemical conversions of RNA before sequencing library preparation. Furthermore, analyzing RNA editing patterns from transcriptomic data provides an additional layer of information about the epitranscriptome. As the significance of epitranscriptomics, particularly RNA editing, gains recognition in various fields of biology and medicine, there is a growing interest in detecting RNA editing sites (RES) by analyzing RNA-seq data. To cope with this increased interest, several bioinformatic tools are available. However, each tool has its advantages and disadvantages, which makes the choice of the most appropriate tool for bench scientists and clinicians difficult. Here, we have benchmarked bioinformatic tools to detect RES from RNA-seq data. We provide a comprehensive view of each tool and its performance using previously published RNA-seq data to suggest recommendations on the most appropriate for utilization in future studies. |
format | Online Article Text |
id | pubmed-10527054 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-105270542023-09-28 Benchmarking RNA Editing Detection Tools Morales, David Rodríguez Rennie, Sarah Uchida, Shizuka BioTech (Basel) Review RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identified: (1) the most frequent, adenosine to inosine (A-to-I); and (2) the less frequent, cysteine to uracil (C-to-U) RNA editing. Unlike other epitranscriptomic marks, RNA editing can be readily detected from RNA sequencing (RNA-seq) data without any chemical conversions of RNA before sequencing library preparation. Furthermore, analyzing RNA editing patterns from transcriptomic data provides an additional layer of information about the epitranscriptome. As the significance of epitranscriptomics, particularly RNA editing, gains recognition in various fields of biology and medicine, there is a growing interest in detecting RNA editing sites (RES) by analyzing RNA-seq data. To cope with this increased interest, several bioinformatic tools are available. However, each tool has its advantages and disadvantages, which makes the choice of the most appropriate tool for bench scientists and clinicians difficult. Here, we have benchmarked bioinformatic tools to detect RES from RNA-seq data. We provide a comprehensive view of each tool and its performance using previously published RNA-seq data to suggest recommendations on the most appropriate for utilization in future studies. MDPI 2023-08-26 /pmc/articles/PMC10527054/ /pubmed/37754200 http://dx.doi.org/10.3390/biotech12030056 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Morales, David Rodríguez Rennie, Sarah Uchida, Shizuka Benchmarking RNA Editing Detection Tools |
title | Benchmarking RNA Editing Detection Tools |
title_full | Benchmarking RNA Editing Detection Tools |
title_fullStr | Benchmarking RNA Editing Detection Tools |
title_full_unstemmed | Benchmarking RNA Editing Detection Tools |
title_short | Benchmarking RNA Editing Detection Tools |
title_sort | benchmarking rna editing detection tools |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10527054/ https://www.ncbi.nlm.nih.gov/pubmed/37754200 http://dx.doi.org/10.3390/biotech12030056 |
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