The McGenus and TT2NE algorithms output predictions of RNA secondary structures with pseudoknots, based on penalizing or restricting the topological genus of the pairing graphs. The topological genus is an indicator of the complexity of the topology of the pairing .
The McGenus algorithm performs a stochastic Monte Carlo search in pairing space for sequences of up to 1000 bases .
The TT2NE algorithm performs an exhaustive or partially exhaustive search in pairing space for sequences of up to respectively 100 or 225 bases .
To obtain the executable of McGenus, please contact: email@example.com or firstname.lastname@example.org or email@example.com .
1. M. Bon and H. Orland, Prediction of RNA secondary structures with pseudoknots, Physica A (2010).
Link to article
2. M. Bon, C. Micheletti and H. Orland, McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots, Nucleic Acids Research (2012) Link to article
3. M. Bon and H. Orland, TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots, Nucleic Acids Research (2011) Link to article
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