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The RNAprobing web server will predict a vector of perturbation energies which minimizes the differences between predicted and observed pairing probabilities. Current limit is 1000nt.

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

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 Fold algorithms and basic options 
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Method used to derive pairing probabilities help
Additional parameters for the method defined above help
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Underlying principlies can be found in:
Katherine E. Deigan, Tian W. Li, David H. Mathews, Kevin M. Weeks Accurate SHAPE-directed RNA structure determination. PNAS, 106:97-102, 2009.
Kourosh Zarringhalam, Michelle M. Meyer, Ivan Dotu, Jeffrey H. Chuang, Peter Clote. Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction. PLOS ONE, 7(10), 2012.
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler, Manolis Kellis. RNA folding with soft constraints: reconciliation of probing data and thermodynamics secondary structure prediction. Nucleic Acids Research, 40(10):4261-4272, 2012.