VIENNARNA : RNAfold - calculate secondary structures of RNAs (Hofacker, Fontana, Bonhoeffer, Stadler)

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RNA Sequences File (format)

Calculate the partition function and base pairing probability matrix (-p)

Advanced rnafold form

Some explanations about the options

Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
You may enter in the text area a database entry code, or an accession number, in this form:


I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188

A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994

M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-148

J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-192

D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London

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