MicroRNAs (miRNAs) are ~22 nt small non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3'UTR seed sequences. We present MicroRNAEngine, a pure-Python pipeline for miRNA target prediction and regulatory network analysis.
Long non-coding RNAs (lncRNAs) regulate gene expression through diverse mechanisms including chromatin remodeling, transcriptional regulation, and post-transcriptional control. We present LncRNAEngine, a pure-Python pipeline for lncRNA regulatory analysis.
Circular RNAs (circRNAs) are covalently closed RNA molecules generated by back-splicing that function as miRNA sponges, protein scaffolds, and translation templates. We present CircularRNAEngine, a pure-Python pipeline for circRNA analysis.
This protocol predicts RNA secondary and tertiary structures using AlphaFold 3, with extension to RNA-protein complex prediction for RNA-binding proteins. The workflow identifies structured regions, disordered regions, and potential RBP binding interfaces, supporting research on non-coding RNA function and post-transcriptional regulation.