Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China.
Department of Pharmacy, China Jiliang University, Hangzhou 310000, China.
Int J Mol Sci. 2023 Feb 14;24(4):3822. doi: 10.3390/ijms24043822.
Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5' and 3' ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively.
环状 RNA（circRNAs）是一类新型的非编码 RNA，与线性 RNA 不同，它们形成一个共价闭环，没有 5' 和 3' 末端。越来越多的证据表明，环状 RNA 在生命过程中发挥着重要作用，在临床和研究领域具有巨大的潜在意义。环状 RNA 结构和稳定性的准确建模对我们理解它们的功能和开发基于 RNA 的治疗方法具有深远的影响。cRNAsp12 服务器提供了一个用户友好的网络界面，可根据序列预测环状 RNA 的二级结构和折叠稳定性。通过基于螺旋的景观分区策略，该服务器为每个集合生成不同的结构集合，并使用递归分区函数计算和回溯算法预测每个集合的最小自由能结构。对于在有限的结构集合中的结构预测，该服务器还为用户提供了设置碱基对强制和/或强制未配对碱基的结构约束的选项，以便仅枚举符合条件的结构。
