RNAdos

What is RNAdos?

RNAdos calculates the density of states for an RNA sequence. Where most RNA folding tools return a single minimum free energy (MFE) structure, RNAdos asks a different question: for each energy level, how many distinct secondary structures exist? The result is a complete profile of the RNA's energy landscape.

This matters because the MFE structure is not always the dominant fold. An RNA molecule with thousands of alternative structures clustered near the MFE occupies a broad, flat energy landscape where no single structure dominates the ensemble. Conversely, a molecule with very few near-MFE states has a sharp, funnel-like landscape and folds reliably into its predicted structure. RNAdos quantifies this distinction directly.

Why density of states matters

The density of states connects RNA sequence to thermodynamic behavior:

• Ensemble characterization: a high state count near the MFE indicates structural promiscuity, while a low count suggests a well-defined fold
• Partition function validation: the density of states can be used to compute thermodynamic quantities (free energy, heat capacity) from first principles
• Riboswitch and regulatory RNA analysis: functional RNAs that switch between conformations often have energy landscapes with two or more competing basins, visible as peaks in the density of states at distinct energy levels
• Sequence design evaluation: when designing RNA sequences with tools like RNAinverse, the density of states reveals whether a designed sequence folds uniquely into the target structure or has many competing alternatives

How to use RNAdos online

RNAdos on ProteinIQ accepts a single RNA sequence in FASTA or plain-text format, runs the ViennaRNA RNAdos program on cloud infrastructure, and returns representative structures with per-band state counts. No local installation of the ViennaRNA package is required.

Input

Input	Description
RNA Sequence	One RNA sequence in FASTA or plain nucleotide format, up to 100 nucleotides. RNAdos operates on a single sequence per job.

Supported file formats: .fasta, .fa, .txt

Settings

Density-of-states options

Setting	Type	Default	Description
Maximum energy band	text	default	Upper bound on the energy range for the density-of-states calculation. Leave blank to let RNAdos determine the range automatically.
Temperature	slider (0-100)	37	Folding temperature in degrees Celsius. Affects thermodynamic parameter scaling.
Salt concentration	text	default	Monovalent salt concentration passed to the ViennaRNA energy model.
Parameter file content	textarea	none	Inline ViennaRNA parameter file content. Written to a temporary file and passed via --paramFile.

Energy parameters

Setting	Type	Default	Description
Dangling ends	select	2 (double dangles)	Controls how unpaired nucleotides adjacent to helices contribute to the energy calculation. Mode 0 ignores them, mode 1 considers only one side, mode 2 (default) considers both sides, and mode 3 enables coaxial stacking.

Leaving optional text fields blank preserves the native ViennaRNA CLI defaults.

Output

Column	Description
Sequence ID	FASTA header or auto-generated identifier
Length (nt)	Number of nucleotides in the input sequence
MFE (kcal/mol)	Minimum free energy of the optimal structure
Representative Structure	Dot-bracket notation for a representative structure in each energy band
Energy Band	The energy level (in kcal/mol above the MFE) for this row
State Count	Number of distinct secondary structures that exist within this energy band

Each row in the results table corresponds to one energy band. The MFE row has an energy band of 0; subsequent rows show progressively higher energy levels with their associated state counts.

Computational cost

RNAdos enumerates structures across the full energy landscape, making it the most computationally intensive ViennaRNA tool on ProteinIQ. ProteinIQ accepts sequences up to 100 nucleotides for RNAdos because runtime and memory use grow steeply with sequence length and energy range. This is a ProteinIQ compute limit, not a scientific limit imposed by ViennaRNA. For longer sequences, or when only the MFE or partition function is needed, use RNAfold. For local accessibility along a longer RNA, use RNAplfold.