RNAthor

RNAthor: Automated normalization and analysis of RNA SHAPE and DMS probing data

RNAthor performs automated normalization and statistical analysis of RNA SHAPE and DMS probing data to generate high-quality reactivity profiles for RNA secondary structure prediction using pseudo-energy constraints.

Key Features:

• Automated Normalization: Identifies and removes unreliable data points and normalizes SHAPE and DMS reactivity values for downstream analysis.
• Uniform Scale Normalization: Scales reactivity data to a uniform range compatible with RNA folding algorithms that incorporate pseudo-energy constraints.
• Statistical Analysis: Performs comparative statistical analyses across multiple datasets to detect significant structural differences.

Scientific Applications:

• RNA Secondary Structure Prediction: Integrates normalized SHAPE and DMS reactivity data with computational folding algorithms to refine RNA secondary structure models.
• Comparative Structural Analysis: Compares RNA structural profiles across experimental conditions to identify structural variation.
• Experimental Data Integration: Processes SHAPE and DMS datasets for comprehensive RNA structure analysis.

Methodology:

RNAthor preprocesses SHAPE and DMS probing data by filtering unreliable measurements, applies uniform scale normalization to generate standardized reactivity values, and enables statistical comparison of multiple datasets for integration with RNA secondary structure prediction algorithms using pseudo-energy constraints.