CircCode: A Powerful Tool for Identifying circRNA Coding Ability

Peisen Sun; Guanglin Li

doi:10.3389/fgene.2019.00981

CircCode: A Powerful Tool for Identifying circRNA Coding Ability

Front Genet. 2019 Oct 10:10:981. doi: 10.3389/fgene.2019.00981. eCollection 2019.

Authors

Peisen Sun^{1

2}, Guanglin Li^{1

2}

Affiliations

¹ Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
² College of Life Sciences, Shaanxi Normal University, Xi'an, China.

Abstract

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.

Keywords: bioinformatics; circular RNAs; classification; coding potential; ribosome profiling data; translation.