RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation

Functional RNA molecules are crucial for biological processes from gene regulation to protein synthesis, and analyzing functional motifs and elements is essential for understanding RNA regulation. Building on RegRNA 1.0 and 2.0, we present RegRNA 3.0, a sophisticated meta-workflow that integrates 26 computational tools and 28 databases for annotation, enabling one-step and customizable RNA motif predictions. RegRNA streamlines multi-step analysis and enhances result interpretation with interactive visualizations and comprehensive reporting tools. When provided with an RNA sequence, RegRNA 3.0 generates predictions for RNA functional motifs, RNA interaction motifs, and comprehensive RNA annotations. Specifically, RNA functional motifs include core promoter elements, RNA decay, G-quadruplex, and 14 previous types. RNA interaction motifs include newly added RNA-ligand interactions and RNA-binding protein predictions, along with three previous types. RNA annotation includes RNA family classification, blood exosomes RNA, subcellular localizations, A-to-I editing events, modifications, and 3D structures, along with four previously supported features. RegRNA 3.0 accelerates gene regulation and RNA biology discoveries by offering a user-friendly platform for identifying and analyzing RNA motifs and interactions. The web interface has been improved for intuitive visualizations of predicted motifs and structures, with flexible download options in multiple formats. It is available at http://awi.cuhk.edu.cn/∼RegRNA/.