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.
ProteinIQ provides browser-based access to RNAplot, computing structure layouts without requiring local installation of the ViennaRNA Package.
| 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
| Setting | Description |
|---|---|
Temperature | Folding temperature in degrees Celsius (0-100, default 37). Affects structure prediction when no pre-computed structure is provided. |
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 |
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:
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.
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.
