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.
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
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.
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.
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
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.
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”.
The ViennaRNA Package is a toolkit for RNA secondary-structure prediction and analysis. ProteinIQ supports a curated subset of ViennaRNA 2.7.2 workflows through one tool while preserving default settings and tool semantics.
The unified ViennaRNA tool currently supports:
RNA Sequences: sequence-based workflows such as RNAfold, RNAsubopt, RNALfold, RNAplfold, RNAdos, RNAeval, and RNAinverse start-sequence inputRNA Sequence 1 / RNA Sequence 2: two-sequence workflows such as RNAcofold, RNAduplex, RNAup, and RNAplexAligned RNA Sequences: RNAalifoldTarget Structure: RNAplot, RNAinverse, RNAeval, and RNAdistanceSecond Structure: RNAdistanceTemperature, Disallow lonely pairs, Circular RNA, and Dangling endsCompute partition function is opt-in, not default-oncutoff, opening_energies, and plex_output for RNAplfoldoutput_format for RNAplotrepeat, final, and alphabet for RNAinversedistance, compare, and backtrack for RNAdistanceconcentrations for RNAcofold concentration modeDepending on the selected workflow, the tool returns:
When a workflow generates files, they appear in the Files tab.
2.7.2.