jViz.Rna

jViz.Rna: Interactive RNA Structure Visualization for Researchers

Overview

jViz.Rna is an interactive visualization tool designed to help researchers explore, annotate, and present RNA secondary structures. It combines an intuitive web-based interface with flexible export options, enabling users to move seamlessly from exploratory analysis to publication-ready figures.

Key features

• Interactive drawing: Click-and-drag layout editing with automatic re-arrangement to reduce overlaps.
• Sequence–structure linking: Hover or select nucleotides in the linear sequence view to highlight corresponding positions in the secondary-structure diagram.
• Annotation layers: Add colored regions, labels, and custom notes for motifs, binding sites, or experimental hits.
• Pairing confidence display: Visualize base-pair probability or reactivity scores as line thickness, color gradients, or opacity.
• Import/export compatibility: Accepts common formats (CT, dot-bracket, Vienna, FASTA) and exports SVG/PNG/PDF for figures.
• Scripting/API support: Automate batch rendering, annotate programmatically, or integrate with analysis pipelines.

Typical workflows

1. Import sequence and predicted structure (dot-bracket/Vienna).
2. Use automatic layout to produce an initial diagram.
3. Overlay experimental data (SHAPE/ DMS reactivity, pairing probabilities).
4. Manually adjust layout or annotate regions of interest.
5. Export high-resolution figures or PNG snapshots for presentations.

Practical tips for researchers

• Start with automatic layout, then unlock and fine-tune problem areas to save time.
• Map experimental reactivity as a color gradient on nucleotides to quickly spot flexible vs. stable regions.
• Use annotation layers to keep notes and hypotheses separate from figure-ready elements.
• Leverage scripting when processing many sequences to ensure consistent styling and reproducibility.
• Export SVG for publication to preserve scalability and allow post-processing in vector editors.

Example use cases

• Visualizing effects of mutations on local structure by comparing paired diagrams side-by-side.
• Preparing figures for papers or talks that show both structure and experimental probing results.
• Teaching RNA secondary structure concepts with an interactive, editable canvas.
• Integrating into pipelines that predict structures and then automatically generate annotated visuals.

Integration and compatibility

jViz.Rna is intended to fit into common RNA analysis ecosystems. It accepts standard prediction outputs from tools like ViennaRNA and can be embedded in web notebooks or called from command-line scripts for automated figure generation.

Limitations and considerations

• jViz.Rna focuses on 2D secondary structure representation; it does not model full 3D folding.
• Very large RNAs may require manual intervention to produce clear, uncluttered layouts.
• Users should verify that imported structures match the sequence (coordinate offsets or naming mismatches can occur).

Getting started

• Prepare sequence and structure files in any accepted format (dot-bracket, CT, Vienna).
• Load files into jViz.Rna, apply automatic layout, and import any experimental reactivity data.
• Adjust annotations and export figures in SVG/PNG/PDF as needed.

Conclusion

jViz.Rna streamlines the process of turning RNA sequences and structure predictions into clear, informative visuals. Its interactivity, annotation capabilities, and export options make it a practical choice for researchers producing figures, exploring hypotheses, or teaching RNA structure concepts.