McGenus / TT2NE
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
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Nucleic Acids Res. 2013 Feb 1;41(3):1895-900. doi: 10.1093/nar/gks1204. Epub 2012 Dec 16.
McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.
Bon M1, Micheletti C, Orland H.
TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots.
Bon M, Orland H.
Nucleic Acids Res. 2011 Aug;39(14):e93. doi: 10.1093/nar/gkr240.