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 only treat sequences of length smaller than 1000.

For sequences smaller than 500 bases, the computation time is less than 10 minutes.
For longer sequences, the computation time may reach one hour.
To obtain the executable of McGenus, please contact: michael.bon@cea.fr or michelet@sissa.it or henri.orland@cea.fr .

Parameters

Maximum genus :
Genus penalty :
Number of optimal structures :

         

Energy model

          Turner energy model
          Our own (unpublished) model

Fold it !

                                             


to enforce only H-pseudoknots of extent less than bases                        

OR

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 the algorithms

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 [1].

The McGenus algorithm performs a stochastic Monte Carlo search in pairing space for sequences of up to 1000 bases [2].

The TT2NE algorithm performs an exhaustive or partially exhaustive search in pairing space for sequences of up to respectively 100 or 225 bases [3].

To obtain the executable of McGenus, please contact: michael.bon@cea.fr or michelet@sissa.it or henri.orland@cea.fr .


References

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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