The RNAcofold web server will predict secondary structures of single stranded RNA or DNA sequences upon dimer formation.

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 these sample sequences.

Paste or type your first sequence here:

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Or upload a file containing the first sequence in FASTA format:

Paste or type your second sequence here:

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Or upload a file containing the second sequence in FASTA format:

 Fold algorithms and basic options 

	minimum free energy (MFE) and partition function (for all species) Calculate the partition function and base pairing probability matrix in addition to the minimum free energy (MFE) structure. In this case, this is done for the two monomers, the two homodimers, and the heterodimer.
	minimum free energy (MFE) and partition function (hetero-dimer only) 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 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)

   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.

 Concentrations 

	Use no concentration parameters RNA-RNA interactions are concentration dependent.Check this radio button if you do not want predicitons for a given set of concentrations.
	Vary concentration (generates concentration dependcy plots) Check this radio button to generate concentration dependency plots. RNAcofold is then called with a predefined concentration file.
	Use user specified concentrations You can enter concentrations in the text-area below, e.g.: 0.0001 00.2

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