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CircCode: A Powerful Tool for Identifying circRNA Coding Ability
Circular RNAs (circRNAs), which play vital roles in many regulatory pathways, are widespread in many species. Although many circRNAs have been discovered in plants and animals, the functions of these RNAs have not been fully investigated. In addition to the function of circRNAs as microRNA (miRNA) d...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795751/ https://www.ncbi.nlm.nih.gov/pubmed/31649739 http://dx.doi.org/10.3389/fgene.2019.00981 |
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author | Sun, Peisen Li, Guanglin |
author_facet | Sun, Peisen Li, Guanglin |
author_sort | Sun, Peisen |
collection | PubMed |
description | Circular RNAs (circRNAs), which play vital roles in many regulatory pathways, are widespread in many species. Although many circRNAs have been discovered in plants and animals, the functions of these RNAs have not been fully investigated. In addition to the function of circRNAs as microRNA (miRNA) decoys, the translation potential of circRNAs is important for the study of their functions; yet, few tools are available to identify their translation potential. With the development of high-throughput sequencing technology and the emergence of ribosome profiling technology, it is possible to identify the coding ability of circRNAs with high sensitivity. To evaluate the coding ability of circRNAs, we first developed the CircCode tool and then used CircCode to investigate the translation potential of circRNAs from humans and Arabidopsis thaliana. Based on the ribosome profile databases downloaded from NCBI, we found 3,610 and 1,569 translated circRNAs in humans and A. thaliana, respectively. Finally, we tested the performance of CircCode and found a low false discovery rate and high sensitivity for identifying circRNA coding ability. CircCode, a Python 3–based framework for identifying the coding ability of circRNAs, is also a simple and powerful command line-based tool. To investigate the translation potential of circRNAs, the user can simply fill in the given configuration file and run the Python 3 scripts. The tool is freely available at https://github.com/PSSUN/CircCode. |
format | Online Article Text |
id | pubmed-6795751 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-67957512019-10-24 CircCode: A Powerful Tool for Identifying circRNA Coding Ability Sun, Peisen Li, Guanglin Front Genet Genetics Circular RNAs (circRNAs), which play vital roles in many regulatory pathways, are widespread in many species. Although many circRNAs have been discovered in plants and animals, the functions of these RNAs have not been fully investigated. In addition to the function of circRNAs as microRNA (miRNA) decoys, the translation potential of circRNAs is important for the study of their functions; yet, few tools are available to identify their translation potential. With the development of high-throughput sequencing technology and the emergence of ribosome profiling technology, it is possible to identify the coding ability of circRNAs with high sensitivity. To evaluate the coding ability of circRNAs, we first developed the CircCode tool and then used CircCode to investigate the translation potential of circRNAs from humans and Arabidopsis thaliana. Based on the ribosome profile databases downloaded from NCBI, we found 3,610 and 1,569 translated circRNAs in humans and A. thaliana, respectively. Finally, we tested the performance of CircCode and found a low false discovery rate and high sensitivity for identifying circRNA coding ability. CircCode, a Python 3–based framework for identifying the coding ability of circRNAs, is also a simple and powerful command line-based tool. To investigate the translation potential of circRNAs, the user can simply fill in the given configuration file and run the Python 3 scripts. The tool is freely available at https://github.com/PSSUN/CircCode. Frontiers Media S.A. 2019-10-10 /pmc/articles/PMC6795751/ /pubmed/31649739 http://dx.doi.org/10.3389/fgene.2019.00981 Text en Copyright © 2019 Sun and Li http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Sun, Peisen Li, Guanglin CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title | CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title_full | CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title_fullStr | CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title_full_unstemmed | CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title_short | CircCode: A Powerful Tool for Identifying circRNA Coding Ability |
title_sort | circcode: a powerful tool for identifying circrna coding ability |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795751/ https://www.ncbi.nlm.nih.gov/pubmed/31649739 http://dx.doi.org/10.3389/fgene.2019.00981 |
work_keys_str_mv | AT sunpeisen circcodeapowerfultoolforidentifyingcircrnacodingability AT liguanglin circcodeapowerfultoolforidentifyingcircrnacodingability |