The RNAinverse web server will search for sequences folding into a predefined structure.

Simply paste or upload your sequences 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 structure/sequence pair.

Paste or type your structure in bracket format here:

[clear]

Paste or type a start sequence for the search here (optional):	[clear]
Any symbols except AUCGTXKI will indicate a random base. Use lower case characters in positions that should be kept fixed.

 Fold algorithms and basic options 

	minimum free energy (MFE) and partition function Calculate the partition function and base pairing probability matrix in addition to the minimum free energy (MFE) structure.
	minimum free energy (MFE) only Predicts only the optimal secondary structure.
	no GU pairs at all Disallow GU wobble pairs in prediction.

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.

 Other options 

	threshold for stop condition when using partition function folding. If the difference between the ensemble free energy and MFE becomes smaller than this threshold, computation is stopped.
1 5 10 50 100	number of sequences to be generated Choose this option to generate more sequences in one run.

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