The HotKnots program predicts secondary structures of RNA molecules with or without pseudoknots. The HotKnots algorithm has been described by Ren et al, 2005. New parameters have been estimated by Andronescu et al, 2009. The latest version is 2.0.
- Version 2.0 of the Hotknots Package, as used by Andronescu et al, 2009:
- Version 1.0, as used by Ren et al, 2005:
- Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005).
HotKnots: heuristic prediction of RNA secondary structures including
pseudoknots. RNA, 11(10), 1494--1504.
Andronescu, M., Pop, C., and Condon, A., Improved energy parameters for RNA pseudoknotted secondary structure prediction, RNA. 2010 Jan;16(1):26-42.