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Open-source bioinformatics tools for the analysis of SHAPE studies to predict RNA structure

SHAPEware is a set of computational tools for researchers to explore and predict the secondary structure and potential ligand binding sites in an RNA using SHAPE (Selective 2′ Hydroxyl Acylation analyzed by Primer Extension) methodologies.

SHAPE is the most widely used approach for probing RNA secondary structure and was developed by Kevin Weeks, Ph.D., and colleagues at the University of North Carolina in 20051. SHAPE studies provide scientists with experimental assessment of predicted loops, bulges and pockets in the two-dimensional structures of RNA. The resulting integrated structural prediction enables biological insight into RNA function and detection of ligand binding sites within the RNA.

1. Smola, MJ, et. al., Nature Protocols. Vol 10 No. 11, 2015.