Department of Cardiology, The Sixth Medical Centre, Chinese PLA General Hospital, Beijing, 100853, People's Republic of China.
Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, 400042, People's Republic of China.
Sci Rep. 2024 Aug 16;14(1):19040. doi: 10.1038/s41598-024-69744-2.
Protein-encoding circular RNAs (circRNAs) are newly identified RNA molecules characterized by intense interaction with translating ribosome. Emerging evidence has implicated physiological and pathological significance of these non-canonical RNAs, yet a large body of them remains unidentified. Due to limited tools at hand, we developed CircProPlus, an automated computational pipeline for de novo detection of translated circRNAs. In comparison to previously established CircPro, CircProPlus adjusts the overall workflow and integrates more robust implements for achieving easier accessibility, higher flexibility and productivity. In present study, we tested the performance of CircProPlus when using different circRNA-detecting implements (i.e., CIRI2, CirComPara2) in the evaluation of coding ability of circRNAs. Results showed that CirComPara2, a state-of-the-art algorithm, consistently outperformed CIRI2 when coupled with CircProPlus in testing real data collected from different RNA libraries and species, which highlighted its potency in data mining of circRNAs with protein-coding potential.
蛋白质编码的环状 RNA（circRNAs）是新鉴定的 RNA 分子，其特征是与翻译核糖体强烈相互作用。越来越多的证据表明这些非规范 RNA 具有生理和病理意义，但其中很大一部分仍未被识别。由于手头的工具有限，我们开发了 CircProPlus，这是一种用于从头检测翻译环状 RNA 的自动化计算流程。与以前建立的 CircPro 相比，CircProPlus 调整了整体工作流程，并集成了更强大的工具，以实现更简单的访问、更高的灵活性和生产力。在本研究中，我们测试了 CircProPlus 在使用不同的环状 RNA 检测工具（即 CIRI2、CirComPara2）评估环状 RNA 的编码能力时的性能。结果表明，CirComPara2 是一种最先进的算法，当与 CircProPlus 结合使用时，在测试来自不同 RNA 文库和物种的真实数据时，其性能始终优于 CIRI2，这突出了其在具有蛋白质编码潜力的环状 RNA 数据挖掘中的强大功能。
