The barriers web server will give you insights into the folding kinetics of a RNA molecule. It first calls RNAsubopt to calculate suboptimal structures within a predefined energy range (limited to roughly 10 million 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.

Paste or type your sequence here:

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Or upload a file in FASTA format:

 Basic options 

	maximal number of lowest local minima Maximal number of local minima. Default value is 50, maximum is 500 (Values above 500 will be reduced to 500)
	consider only minima with a barrier higher than Merge local minima that have a barriers height less than this threshold.
	no GU pairs at the end of helices Apart from the canonical AU and GC pairs RNA frequently forms (weaker) GU pairs. Check this box to disallow GU at the end of helices.
	avoid isolated base pairs Predicted structures can contain isolated base pairs (helices of length 1), which may be undesirable. Check this box to avoid such lonely pairs.

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.

Notification via e-mail upon completion of the job (optional):