RNAProbe

RNAProbe processes and normalizes chemical RNA probing data to quantify nucleotide reactivities and inform RNA secondary structure prediction.

Key Features:

• Normalization and Analysis: Automated normalization of chemical probing data according to an established protocol, including handling of low-pass SHAPE, DMS, and CMCT probing with modification sites detected by capillary electrophoresis.
• Secondary Structure Prediction: Integration of recognized secondary structure prediction methods that incorporate normalized probing reactivities to guide folding models.
• Visualization Tools: Generation of images representing RNA secondary structures and reactivity heatmaps to display nucleotide susceptibility to modification.
• Data Summarization and Interoperability: Export of summarized results in spreadsheet format and provision of normalized reactivities in text files for downstream bioinformatics workflows.

Scientific Applications:

• RNA structure–function analysis: Quantitative reactivity data and structure models to study relationships between RNA structure and function.
• Cellular RNA studies: Analysis of chemical probing datasets (SHAPE, DMS, CMCT) to investigate RNA roles in cellular processes.
• Translational research: Provision of RNA structural information useful for applications in drug discovery and molecular diagnostics.

Methodology:

Automatic analysis of chemical probing output data, normalization based on established protocols, and utilization of recognized secondary structure prediction methods; handles modification-site data detected by capillary electrophoresis.