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Front. Genet. | doi: 10.3389/fgene.2019.00981

CircCode: a powerful tool for identifying circRNA coding ability

Li guanglin1* and  Sun Peisen1
  • 1Shaanxi Normal University, China

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 3610 and 1569 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.

Keywords: bioinformatics, circular RNAs, ribosome profiling data, translation, coding potential, Classification

Received: 21 Jun 2019; Accepted: 13 Sep 2019.

Copyright: © 2019 guanglin and Peisen. 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.

* Correspondence: Mx. Li guanglin, Shaanxi Normal University, Xi'an, 710062, Shaanxi Province, China, glli@snnu.edu.cn