IntaRNA predicts interactions between two RNA molecules, e.g. a non-coding RNA (ncRNA) and a mRNA. The scoring is based on hybridization free energy and accessibility of the interaction sites in both molecules.
- Vienna RNA package
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IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Anke Busch, Andreas S. Richter, Rolf Backofen
Bioinformatics, 2008, 24(24), 2849-56