ViennaRNA

Predict and analyze RNA secondary structures.

Add your input molecules to get started

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Configure input settings on the left, then click "Submit"

Related tools

RNAdos

RNAdos

RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.

RNAeval

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

RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.

RNALfold

RNALfold

RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.

RNAplfold

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

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

RNAcofold

RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.

RNAdistance

RNAdistance

RNAdistance compares RNA secondary structures using the selected upstream ViennaRNA distance representation and comparison mode.

RNAduplex

RNAduplex

RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.

RNAplex

RNAplex

RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.

What is ViennaRNA?

The ViennaRNA Package is a toolkit for RNA secondary-structure prediction and analysis. ProteinIQ exposes a curated subset of ViennaRNA 2.7.2 workflows through one wrapper while preserving upstream defaults and tool semantics.

Available methods

The unified ViennaRNA tool currently exposes:

  • RNAfold: MFE folding with optional partition-function ensemble metrics
  • RNAsubopt: Suboptimal structures within an energy band
  • RNALfold: Local folding for long sequences
  • RNAplfold: Local accessibility and CLI-generated probability artifacts
  • RNAplot: Plot a supplied sequence-structure pair
  • RNAcofold: Joint folding of two interacting RNAs with optional concentration mode
  • RNAduplex: Fast duplex prediction
  • RNAdos: Density-of-states analysis
  • RNAup: Accessibility-aware interaction analysis
  • RNAplex: Fast query-target interaction prediction
  • RNAalifold: Consensus folding from aligned sequences
  • RNAinverse: Inverse folding from structure plus starting sequence/constraints
  • RNAeval: Sequence-structure energy evaluation
  • RNAdistance: Structure distance calculation with configurable distance and compare modes

Inputs

  • RNA Sequences: sequence-based workflows such as RNAfold, RNAsubopt, RNALfold, RNAplfold, RNAdos, RNAeval, and RNAinverse start-sequence input
  • RNA Sequence 1 / RNA Sequence 2: two-sequence workflows such as RNAcofold, RNAduplex, RNAup, and RNAplex
  • Aligned RNA Sequences: RNAalifold
  • Target Structure: RNAplot, RNAinverse, RNAeval, and RNAdistance
  • Second Structure: RNAdistance

Shared settings

  • Shared folding controls include Temperature, Disallow lonely pairs, Circular RNA, and Dangling ends
  • Compute partition function is opt-in, not default-on
  • Method-specific controls are exposed only for the workflows that support them, such as:
    • cutoff, opening_energies, and plex_output for RNAplfold
    • output_format for RNAplot
    • repeat, final, and alphabet for RNAinverse
    • distance, compare, and backtrack for RNAdistance
    • concentrations for RNAcofold concentration mode

Output

Depending on the selected workflow, the wrapper returns:

  • spreadsheet rows
  • downloadable plot files
  • downloadable accessibility and interaction reports
  • optional ensemble metrics when partition-function mode is enabled
  • structure-distance rows
  • concentration/equilibrium rows for RNAcofold concentration mode

When a workflow generates files, they appear in the Files tab.

Notes

  • The wrapper is pinned to ViennaRNA 2.7.2.
  • Partition-function calculations are opt-in where upstream treats them as optional.
  • RNAplot renders supplied structures; it does not fold the input sequence first.