inteRNA is the first program that aims to compute the joint structure prediction of two given RNA sequences through minimizing their total free energy, which, is a function of the topology of the joint structure. The algorithmic foundations of inteRNA were introduced by Alkan et al.(RECOMB 2005). inteRNA aims to minimize the joint free energy under a number of energy models with growing complexity. The default energy model is based mostly on stacked pair energies given by Mathews et al.(J. Mol. Biol. 1999) – the free energy model employed by Mfold. Because there is very little thermodynamic information on kissing loop sequences in the literature, inteRNA employs the approach used by Rivas and Eddy(J. Mol. Biol. 1999) to differentiate the thermodynamic parameters of “external” bonds from the “internal” bonds.
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“Time and space efficient RNA-RNA interaction prediction via sparse folding“,
Raheleh Salari, Mathias Mohl, Sebastian Will, S. Cenk Sahinalp, and Rolf Backofen.
RECOMB’10, Research in Computational Molecular Biology, (2010).