Vienna RNA Websuite

Vienna RNA Websuite provides computational methods for folding, designing, and analyzing RNA sequences to predict secondary structures, RNA-RNA interactions, and folding landscapes.

Key Features:

• RNA Folding: Supports folding of single RNA sequences and aligned sequences to predict secondary structures.
• Prediction of RNA-RNA Interactions: Predicts interactions between different RNA molecules to analyze intermolecular base pairing.
• Design of Sequences with a Given Structure: Designs RNA sequences that fold into specified secondary structures.
• Analysis of Folding Landscapes: Analyzes folding landscapes and thermodynamic properties using the barriers program.
• Structural RNA Alignments using LocARNA: Performs structural alignments of RNA sequences with LocARNA for comparative and evolutionary analyses.

Scientific Applications:

• Functional RNA analysis: Enables investigation of the functional roles of RNA molecules via secondary-structure prediction.
• Regulatory network studies: Supports study of RNA-RNA interactions relevant to regulatory networks and molecular mechanisms.
• Structure–function investigations: Facilitates design-based studies of RNA structure–function relationships.
• Thermodynamic and dynamic analysis: Provides insights into thermodynamic stability and folding dynamics through folding landscape analysis.
• Comparative and evolutionary studies: Allows structural alignments to support comparative analyses and evolutionary studies of RNA families.

Methodology:

Computational methods explicitly include folding of single and aligned sequences to predict secondary structures, prediction of RNA-RNA interactions, design of sequences that fold into specified structures, analysis of folding landscapes using the barriers program, and structural alignments using LocARNA.