Welcome to the RNAalifold web server. It will predict a consensus secondary structure of a set of aligned sequences. Current limits are 3000 nt and 300 sequences for an alignment.

Simply paste or upload your alignment(s) below and click Proceed. Accepted alignment formats are CLUSTAL W and FASTA (will be detected automatically). To get more information on the meaning of the options click the symbols. You can test the server using this sample alignment.

Paste your alignment(s) here:

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Show constraint folding

| : paired with another base		> : base i is paired with a base j>i
x : base must not pair		< : base i is paired with a base j<i
. : no constraint at all		matching brackets ( ): base i pairs base j

Paste or type constraint here:

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Or upload a file:

 RNAalifold version 

	new RNAalifold with RIBOSUM scoring (Bernhart SH et al. 2008) The new RNAalifold version with better gap character handling. In addition ribosum scoring matrices are used. The matrix is chosen automatically according to the minimal and maximal pairwise identities of the sequences in the alignment file.
	new RNAalifold (Bernhart SH et al. 2008) The new RNAalifold version with better gap character handling.
	old RNAalifold (Hofacker IL et al. 2002) The old RNAalifold version where gaps are treated as characters.

 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.
	output "most informative sequence" instead of simple consensus For each column of the alignment output the set of nucleotides with frequency greater than average in IUPAC notation.
	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.

   Weight of covariance term

Determines the relative strength of secondary structure energy vs covariance term. Values between 0 and 10 may be specified.

   Penalty for non-compatible sequences

Determines how strongly pairs that cannot be formed by all sequences are penalized within the covariance term.

 Output options 

	interactive RNA secondary structure plot Generates an interactive SVG-File displaying reliability information.
	RNA secondary structure plots with reliability annotation (Partition function folding only) Colorize a secondary structure plot with reliability annotation from positional entropy and base-pairing probabilities.
	Mountain plot A mountain plot represents a secondary structure in a plot of height versus position, where the height m(k) is given by the number of base pairs enclosing the base at position k. I.e. loops correspond to plateaus (hairpin loops are peaks), helices to slopes. Check this box to produce a PNG image with the mountain plot.

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