TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots

Michaël Bon (1) , Henri Orland (1)

1 IPHT - Institut de Physique Théorique - UMR CNRS 3681

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions. Analysis of TT2NE's incorrect predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php.

Domains: Molecular biology

Michaël Bon, Henri Orland. TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots. Nucleic Acids Research, 2011, 39, pp.e93. ⟨10.1093/nar/gkr240⟩. ⟨cea-00666032⟩