The RNAeval web server calculates the energy of a RNA sequence on a given secondary structure. You can use it to get a detailed thermodynamic description (loop free-energy decomposition) of your RNA structures.

Simply paste or upload your sequence below and click Proceed. To get more information on the meaning of the options click the symbols. You can test the server using this sample sequence/structure pair.

Paste or type your sequence here:

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Paste or type your structure here:

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Show advanced options

 Advanced folding options 

Dangling end options

Dangling end energies are stabilizing energies assigned to unpaired bases adjacent to a helix in multi-loops and free ends.

   no dangling end energies
   unpaired bases can participate in at most one dangling end (MFE folding only)
   dangling energies on both sides of a helix in any case
   allow coaxial stacking of adjacent helices in multi-loops (MFE folding only)

Energy Parameters

Change the energy parameter file used to predict secondary structures.

   RNA parameters (Turner model, 2004)
   RNA parameters (Turner model, 1999)
   RNA parameters (Andronescu model, 2007)
   DNA parameters (Matthews model, 2004)

Other Parameters
   rescale energy parameters to given temperature (C)

The energy parameters used in the calculation have been measured at 37C. Parameters at other temperatures can be extrapolated, but for temperatures far from 37C results will be increasingly unreliable.

   assume RNA molecule to be circular

RNA molecule is treated to be circular. Since Vienna RNA package v. 1.7 this options is also valid for partition function folding.

   Incoorporate G–Quadruplex formation into the structure prediction algorithm

Incorporate G–Quadruplex formation into the structure prediction algorithm