RNA-align: Quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

Abstract

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 coarsegrained 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/.