RNAbor: a web server for RNA structural neighbors

RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning δ-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A δ-neighbor is a structure that differs from the input structure by exactly δ base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly δ base pairs. For each distance δRNAbor computes the density of δ-neighbors, the number of δ-neighbors, and the MFE structure, or MFE (δ) structure, among all δ-neighbors. RNAbor can be used to study possible folding pathways, to determine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is available at http://bioinformatics.bc.edu/clotelab/RNAbor.