CircCode: A Powerful Tool for Identifying circRNA Coding Ability
CircCode: A Powerful Tool for Identifying circRNA Coding Ability
复制标题
CircCode：识别 circRNA 编码能力的强大工具
DOI：
10.3389/fgene.2019.00981
复制
发表时间：
2019-10-10
影响因子：
3.7
通讯作者：
Li, Guanglin
中科院分区：
文献类型：
--
作者：
Sun, Peisen;Li, Guanglin
环状RNA（circRNA）广泛存在于许多物种中，在许多调控途径中发挥重要作用。尽管在植物和动物中发现了许多circRNA，但这些RNA的功能尚未得到充分研究。除了circRNA作为microRNA（miRNA）诱饵的功能外，circRNA的翻译潜力对于研究其功能也很重要;然而，很少有工具可用于鉴定其翻译潜力。随着高通量测序技术的发展和核糖体谱分析技术的出现，使得高灵敏度鉴定circRNA的编码能力成为可能。为了评估circRNA的编码能力，我们首先开发了CircCode工具，然后使用CircCode研究来自人类和拟南芥的circRNA的翻译潜力。基于从NCBI下载的核糖体图谱数据库，我们在人类和A. thaliana，分别。最后，我们测试了CircCode的性能，发现它具有较低的错误发现率和较高的识别circRNA编码能力的灵敏度。CircCode是一个基于Python 3的框架，用于识别circRNA的编码能力，也是一个简单而强大的基于命令行的工具。为了研究circRNA的翻译潜力，用户可以简单地填写给定的配置文件并运行Python 3脚本。该工具可在https://github.com/PSSUN/CircCode上免费获得。
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.