Structural RNA modules consist of sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs recurrently observed in RNA families throughout the phylogeny. They play central roles as architectural organizers and sites of ligand binding in RNA molecules. Here we describe a computational tool for the detection of structural modules in single and multiple RNA sequences Structural RNA modules consist of sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs recurrently observed in RNA families throughout the phylogeny. They play central roles as architectural organizers and sites of ligand binding in RNA molecules. Here we describe a computational tool for the detection of structural modules in single and multiple RNA sequences
in the absence of any other information. We systematically search four of the most common RNA modules (G-bulges, Kink-turns, C-loops and tandem-GAs), in the 1,444 publicly available RNA alignments of RFam where we've found 21 yet unreported modules. Finally we'll discuss the strengths and limitations of the approach and some open problems in the domain of structural module discovery.