RNAplot

What is RNAplot?

RNAplot is the ViennaRNA Package program for turning an RNA sequence and an already specified secondary structure into a two-dimensional structure graph. It does not predict base pairs or calculate folding energy. Instead, it assigns nucleotide coordinates to the supplied dot-bracket structure and writes a diagram or an exchange file that can be viewed, edited, or used in downstream analysis.

This separation is useful when the structure came from an experiment, a comparative analysis, or another prediction method. For example, RNAfold can provide a minimum-free-energy structure, while RNAplot provides a publication-ready representation of the selected structure. The rendered graph describes the submitted pairing pattern, not a new thermodynamic prediction.

How to use RNAplot online

ProteinIQ runs RNAplot on one RNA sequence and its matching dot-bracket structure, then returns the chosen diagram file for download. Paste or upload the sequence in FASTA or plain text, provide one valid structure of the same length, select EPS, SVG, GML, XRNA, or SSV, and receive the rendered secondary-structure artifact plus a record of the submitted inputs.

Inputs

Input	Description
RNA Sequence	One RNA sequence, entered as plain sequence or a single FASTA record. .fasta, .fa, and .txt files are accepted, up to 10 MB. A FASTA header becomes the sequence ID shown in the result.
Target Structure	One dot-bracket structure in plain text, up to 1 MB. Its length must exactly equal the sequence length. Dots represent unpaired nucleotides; matched ( and ), [ and ], or { and } characters represent paired positions.

For a 16-nucleotide hairpin, a structure such as (((.(((...)))))) has one character per nucleotide. Whitespace is ignored, but unbalanced brackets, an RNA sequence pasted into the structure field, or a sequence-structure length mismatch stop the job before rendering.

RNAplot accepts one sequence-structure pair per job. It is intended for a known structure, rather than batch folding or an RNA multiple-sequence alignment.

Output format

Setting	Description
Output format	The downloaded native RNAplot format. EPS is the default and is suited to print-oriented vector figures. SVG is a scalable web and vector-graphics format. GML stores the structure graph for graph-oriented software. XRNA creates an XRNA save file for further editing. SSV is the structure-data format offered by RNAplot for compatible downstream software.

ProteinIQ currently uses RNAplot's standard rendering behavior and offers only the file-format choice. Layout selection, PostScript annotation macros, alignment visualization, and covariance annotation are not settings in this workflow.

Results

The Results table preserves the submitted record and confirms which format was rendered.

Column	Meaning
Sequence ID	FASTA identifier, or the assigned identifier for plain sequence input.
Sequence	RNA sequence used for the plot.
Length	Number of nucleotides in the sequence.
Structure	Validated dot-bracket structure used to generate the graph.
Output Format	Selected RNAplot file format.

The Files tab contains the generated plot artifact. SVG is generally the most convenient choice for browser viewing and editing in vector-graphics software. EPS is appropriate when an existing publication workflow expects PostScript. GML, XRNA, and SSV are exchange formats, so their practical value depends on the software that will read the file next.

How RNAplot works

RNAplot reads the sequence and its pairing pattern, interprets the dot-bracket notation as an RNA secondary-structure graph, and computes coordinates for the nucleotides. ViennaRNA supports several layout algorithms, with Naview as its standard command-line layout. The resulting geometry is then serialized in the selected output format.

The drawing is structural rather than quantitative. Stem lengths, loops, and the arrangement of paired bases make the pairing pattern legible, but spacing and curvature are layout decisions. A more compact-looking stem or loop is not evidence of greater stability, and the figure does not contain base-pair probabilities, free energies, or confidence scores.

Dot-bracket input records nested secondary structure. Bracket types can distinguish pair classes in the notation, but an input still has to be properly nested to pass validation. Complex tertiary contacts and pseudoknots may need a specialized representation or a dedicated visualization workflow.

Choosing RNAplot and related RNA tools

Use RNAplot after the secondary structure is already known and the goal is a downloadable diagram. It is a poor substitute for a folding method because it does not choose between competing structures or score their stability.

• For an MFE structure and folding free energy from one sequence, use RNAfold.
• For a sequence designed to match a target secondary structure, use RNAinverse, then render a selected candidate with RNAplot.
• For the energy of a particular sequence-structure pair, use RNAeval.
• For local accessibility and pairing probabilities along a longer RNA, use RNAplfold.

When a figure comes from RNAfold or another predictor, preserve the exact dot-bracket string used for the plot. Rendering a different candidate structure, even for the same sequence, produces a different biological hypothesis rather than a cosmetic variation.