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Motivation Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. Results We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. Availability and implementation https://zhanglab.ccmb.med.umich.edu/RNA-align/. Supplementary information Supplementary data are available at Bioinformatics online.

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Riboswitches are RNA residue segments located in untranslated regions of messenger RNAs. These folded segments directly bind ligands through shape complementarity and specific interactions in cells and alter the expression of genes at the transcriptional or translational level through conformation change. Using the recently developed systematic helix-based computational method to predict the cotranscription folding kinetics, we theoretically studied the cotranscription folding behavior of the Bacillus subtilis pbuE riboswitch in the absence and presence of the ligand. The ligand concentration, the transcription speed, and the transcription pausing are incorporated into the method. The results are in good agreement with the experimental results. We find that there are no obvious misfolded structures formed during the transcription and the formation of the ligand bound state is rate-limited by the association of the ligand and the RNA. For this kinetically driven riboswitch, the ligand concentration, the transcription speed, and the transcription pausing are coupled to perform regulatory activity.