CAFA

CAFA analyzes capillary electrophoresis data from chemical and enzymatic footprinting to determine nucleic acid structure and protein–DNA interactions.

Key Features:

• Capillary electrophoresis with fluorescent labeling: Processes data derived from capillary electrophoresis of fluorophore-labeled nucleic acids.
• High-Throughput Capability: Handles large-scale structural analyses of nucleic acids to support genomic-scale studies.
• Versatile Mapping Techniques: Supports hydroxyl radical footprinting, dimethyl sulfate (DMS) mapping, and DNase I mapping for chemical and enzymatic probing.
• Robust Quantitation Algorithms: Implements quantitation algorithms to improve accuracy and reproducibility of footprinting analyses.

Scientific Applications:

• RNA Structural Analysis: Infers RNA secondary structure from footprinting data such as hydroxyl radical and DMS mapping.
• Protein–DNA Interaction Studies: Identifies protein binding sites on DNA using DNase I mapping-derived data.
• Genomic-Scale Structural Analysis: Enables large-scale mapping of nucleic acid structures across genomes through high-throughput footprinting data processing.

Methodology:

Processes capillary electrophoresis traces from chemical and enzymatic footprinting using quantitation and data-analysis algorithms to extract nucleic acid structural information.