TRAVeLer

TRAVeLer employs a template-based approach to visualize RNA secondary structures by mapping target structures onto template layouts to produce coherent layouts for large and complex RNAs.

Key Features:

• Template-based visualization: Leverages existing RNA secondary structure layouts as templates to generate visualizations of new RNA molecules.
• Homology-inspired approach: Adopts concepts from homology-based structure prediction methods to guide layout transfer between related structures.
• Tree representation of structures: Transforms both target and template RNA secondary structures into tree representations for comparison.
• Tree edit distance computation: Calculates the tree edit distance between tree representations to identify required modifications.
• Layout transformation operations: Applies layout modification operations to morph a template layout into one representing the target structure.
• Scalability to large and complex RNAs: Produces layouts for large RNA molecules by reusing and adapting existing template layouts, subject to availability of sufficiently similar templates.

Scientific Applications:

• Structural biology: Facilitates interpretation and presentation of RNA secondary structure arrangements for structural analyses.
• Genomics: Supports visualization of large RNA elements identified in genomic studies to aid annotation and comparative analysis.
• Molecular biology: Assists in exploring RNA function and interactions through clearer secondary-structure layouts.
• Evolutionary and comparative analysis: Enables comparison of RNA secondary-structure arrangements across homologous sequences to inform evolutionary relationships.

Methodology:

Transforms target and template RNA secondary structures into tree representations, computes the tree edit distance between them to identify edit operations, and applies layout modification operations to morph the template layout into the target layout.