jViz.RNA

jViz.RNA visualizes and enables interactive editing of RNA secondary structures, including pseudoknots and RNA editing events, to support structural analysis and hypothesis testing.

Key Features:

• Compressed Tree Graphs: jViz.RNA represents RNA structures using compressed tree graphs for faster and more stable visualization of complex molecules.
• Pseudoknot Visualization: It implements a pseudoknot classification system within an RNA graph model to minimize overlap between structural elements and clarify pseudoknotted regions.
• Interactive Editing: The software provides functionality to adjust positioning and connectivity of RNA molecules for dynamic exploration and construction of structures.
• Performance Benchmarking: The software has been benchmarked against other RNA visualization packages, showing improved speed, stability, and interactive responsiveness.

Scientific Applications:

• Pseudoknot analysis: Visualization and classification of pseudoknotted RNA structures to aid structural interpretation.
• RNA editing studies: Representation and editing of RNA sequences undergoing editing processes to examine structural consequences.
• Structure–function and interaction studies: Generation and manipulation of RNA structural models to support investigations of RNA function, structure, and interactions by molecular biologists.

Methodology:

RNA structures are represented with compressed tree graphs and a pseudoknot classification integrated into an RNA graph model, and interactive editing modifies node positioning and connectivity.