Automated, customizable and efficient identification of 3D base pair modules with BayesPairing

RNA structures possess multiple levels of structural organization. A secondary structure, made of Watson–Crick helices connected by loops, forms a scaffold for the tertiary structure. The 3D structures adopted by these loops are therefore critical determinants shaping the global 3D architecture. Earlier studies showed that these local 3D structures can be described as conserved sets of ordered non-Watson–Crick base pairs called RNA structural modules. Unfortunately, the computational efficiency and scope of the current 3D module identification methods are too limited yet to benefit from all the knowledge accumulated in the module databases. We present BayesPairing, an automated, efficient and customizable tool for (i) building Bayesian networks representing RNA 3D modules and (ii) rapid identification of 3D modules in sequences. BayesPairing uses a flexible definition of RNA 3D modules that allows us to consider complex architectures such as multi-branched loops and features multiple algorithmic improvements. We benchmarked our methods using cross-validation techniques on 3409 RNA chains and show that BayesPairing achieves up to ∼70% identification accuracy on module positions and base pair interactions. BayesPairing can handle a broader range of motifs (versatility) and offers considerable running time improvements (efficiency), opening the door to a broad range of large-scale applications.