Folding RNA/DNA hybrid duplexes

Motivation: While there are numerous programs that can predict RNA or DNA secondary structures, a program that predicts RNA/DNA hetero-dimers is still missing. The lack of easy to use tools for predicting their structure may be in part responsible for the small number of reports of biologically relevant RNA/DNA hetero-dimers. Results: We present here an extension to the widely used ViennaRNAPackage (Lorenz et al., 2011) for the prediction of the structure of RNA/DNA hetero-dimers. Availability: http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html Contact: ronny@tbi.univie.ac.at, berni@bioinf.uni-leipzig.de Supplementary Information: Supplementary data are available at Bioinformatics online.