RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res 2007

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 d-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A d-neighbor is a structure that differs from the input structure by exactly d base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly d base pairs. For each distance d RNAbor computes the density of d-neighbors, the number of d-neighbors, and the MFE structure, or MFEd structure, among all d-neighbors. RNAbor can be used to study possible folding pathways, to deter-mine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is availabl