Folding an RNA with pseudoknots

RNA sequence
Write or paste an RNA sequence : list of bases A, C, G, U (upper or lowercase) with or without blanks between the letters.
The server can (at present) only treat sequences of length smaller than 200.

Parameters Maximum genus :
Genus penalty :
Number of optimal structures :



Calculation of the genus of a structure

Upload a structure file in bpseq or ct format

What is the format of your uploaded file ?
          bpseq ct

About TT2NE

TT2NE is a novel algorithm for RNA secondary structure prediction, based on a classification of pseudoknots by their topological genus. To obtain the executable of TT2NE, please contact: michael.bon@cea.fr or henri.orland@cea.fr .


1. M. Bon and H. Orland, Prediction of RNA secondary structures with pseudoknots, Physica A (2010). Link to article
2. 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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