What is RNAplot?
RNAplot generates 2D coordinate layouts for RNA secondary structures. Part of the ViennaRNA Package, it takes sequences and their dot-bracket structures as input and computes nucleotide positions suitable for graphical display. The tool primarily uses the NAView algorithm developed by Bruccoleri and Heinrich in 1988, which produces clear, non-overlapping diagrams where stems appear as ladders and loops remain visually distinct.
Secondary structure visualization transforms abstract bracket notation into interpretable diagrams. A structure like ((((....)))) becomes a stem-loop hairpin where base pairs align vertically and unpaired nucleotides form a loop at the top. RNAplot handles these transformations automatically, positioning each nucleotide to minimize visual clutter.
How to use RNAplot online
ProteinIQ provides browser-based access to RNAplot, computing structure layouts without requiring local installation of the ViennaRNA Package.
Input
| Input | Description |
|---|---|
RNA Sequences | FASTA format or plain sequence text. If no structure is provided, RNAplot first predicts the minimum free energy structure using RNAfold. |
Accepted file formats: .fasta, .fa, .txt
Settings
| Setting | Description |
|---|---|
Temperature | Folding temperature in degrees Celsius (0-100, default 37). Affects structure prediction when no pre-computed structure is provided. |
Results
The output table contains:
| Column | Description |
|---|---|
Sequence ID | Identifier from FASTA header or auto-generated name |
Sequence | The RNA sequence |
Length | Number of nucleotides |
Structure | Dot-bracket notation of the secondary structure |
MFE | Minimum free energy in kcal/mol |
How does RNAplot work?
The NAView algorithm treats RNA secondary structure as a graph where nucleotides are nodes and backbone connections plus base pairs are edges. It computes coordinates through several steps:
- Loop decomposition: The structure is broken into its constituent loops (hairpins, internal loops, bulges, multiloops)
- Radius assignment: Each loop receives a radius proportional to the number of nucleotides it contains
- Angular distribution: Unpaired nucleotides in loops are distributed evenly around the circumference
- Stem placement: Base-paired regions are drawn as parallel lines connecting the loops they join
- Conflict resolution: Overlapping elements are repositioned to minimize intersections
The algorithm runs in nearly linear time relative to sequence length. While it does not guarantee intersection-free drawings for all structures (particularly those with complex multiloops or pseudoknots), it produces readable layouts for the vast majority of RNA structures.
Limitations
RNAplot works with nested secondary structures in dot-bracket notation. Pseudoknots, which create crossing base pairs, cannot be represented in standard bracket notation and require specialized tools.
Very large structures (thousands of nucleotides) may produce layouts where distant regions overlap. For such cases, circular or radial layout variants can provide better visual separation.
The coordinate output represents a static 2D projection. Interactive manipulation, zooming, or annotation requires downstream visualization software.
Related tools
- RNAfold: Predicts the minimum free energy secondary structure, which RNAplot can then visualize
- RNAsubopt: Enumerates alternative structures within an energy range for comparative visualization
- RNAalifold: Computes consensus structures from alignments, useful for visualizing conserved RNA features
- RNAeval: Evaluates the energy of a given structure, helpful for assessing manually drawn or modified diagrams
- ViennaRNA: Access all 14 ViennaRNA methods through a unified interface