Related tools
RNAdos
RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAduplex
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAeval
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
RNALfold
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
RNAplex
RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.
RNAplfold
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
RNAsubopt
RNAsubopt enumerates all RNA secondary structures within a specified energy range above the minimum free energy (MFE). Useful for exploring the structural ensemble and identifying alternative conformations.
RNAup
RNAup predicts accessibility-aware RNA-RNA interactions, reporting opening-energy terms alongside interaction energies and downloadable upstream output files.
ViennaRNA
ViennaRNA exposes a curated set of upstream-faithful ViennaRNA 2.7.2 workflows for RNA folding, density-of-states analysis, interaction prediction, local accessibility, plotting, inverse folding, and structure analysis.
What RNAcofold Does
RNAcofold predicts the joint secondary structure of two interacting RNA molecules. ProteinIQ returns the dimer MFE by default and exposes partition-function ensemble metrics only when explicitly requested.
Inputs
- Provide two RNA sequences in FASTA or plain-sequence format.
- Optional
Concentration tableinput enables concentration-dependent equilibrium calculations.
Settings
Temperature,Disallow lonely pairs, andDangling ends: standard ViennaRNA folding controlsCompute partition function: opt in to ensemble metrics such as ensemble free energy, MFE frequency, ensemble diversity, centroid, MEA, and binding free energyConcentration table: optional upstream concentration mode input
Partition-function mode is off by default to preserve upstream behavior.
Output
The standard structure row reports:
- interaction identifier
- sequence lengths
- dimer structure
- MFE
- optional ensemble metrics when partition-function mode is enabled
When concentration mode is enabled, additional concentration rows report:
- initial concentrations
- equilibrium concentrations for
AA,BB,AB,A, andB - upstream free-energy terms used for the equilibrium calculation