RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
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.
ViennaRNA supports a curated set of scientifically faithful ViennaRNA 2.7.2 workflows for RNA folding, density-of-states analysis, interaction prediction, local accessibility, plotting, inverse folding, and structure analysis.
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
RNAdistance compares RNA secondary structures using the selected native ViennaRNA distance representation and comparison mode.
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.
RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
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.
ViennaRNA supports a curated set of scientifically faithful ViennaRNA 2.7.2 workflows for RNA folding, density-of-states analysis, interaction prediction, local accessibility, plotting, inverse folding, and structure analysis.
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
RNAdistance compares RNA secondary structures using the selected native ViennaRNA distance representation and comparison mode.
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.
Configure inputs to begin
Set options on the left, then click “Submit job”.
RNAplfold computes local accessibility profiles with a sliding-window partition-function workflow. ProteinIQ parses its results directly from the command-line outputs and returns the generated artifacts in the Files tab.
Window size, Maximum span, and Unpaired region length: local folding controlsCutoff: native probability cutoffOpening energies: request opening-energy oriented outputRNAplex output mode: request RNAplex-formatted accessibility outputTemperature: folding temperatureThe results table reports per-position values parsed from the native accessibility file for the selected mode:
_lunpOpening energies mode: opening energies from _openenThe Files tab contains the text artifacts emitted by RNAplfold, such as local accessibility tables and other generated output files for the selected mode.