The RNAup server will predict RNA-RNA interactions. Current limit is 5,000nt per sequence

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:

[clear]

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

Paste or type your second sequence here:

[clear]

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

 Basic options 

	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.
	length of the unstructured region Specifies the length (len) of the region for which the probability of being unpaired is computed.
	maximal length of the region of interaction Determines the maximal length of the region of interaction, i.e. the maximum number of nucleotides a base-pair can span.

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
   dangling energies on both sides of a helix in any case

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.

  include probability of being unpaired in hairpin loops

By default only the full probability (sum of all contributions) of being unpaired is considered. Check this box to get the probability of being unpaired within a hairpin loop.

  include probability of being unpaired in interior loops

By default only the full probability (sum of all contributions) of being unpaired is considered. Check this box to get the probability of being unpaired within a interior loop.

  include probability of being unpaired in external loops

By default only the full probability (sum of all contributions) of being unpaired is considered. Check this box to get the probability of being unpaired within a exterior loop.

  include probability of being unpaired in multi-loops

By default only the full probability (sum of all contributions) of being unpaired is considered. Check this box to get the probability of being unpaired within a multi-loop.

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