SAFA

SAFA quantifies band intensities in nucleic acid chemical mapping gels at single-nucleotide resolution to enable precise analysis of nucleic acid structure and interactions.

Key Features:

• Lane Identification: Identifies lanes in gel images to align analyses with experimental lanes.
• Gel Rectification: Corrects gel-image distortions and standardizes gel geometry for consistent analysis.
• Band Assignment: Assigns bands to specific nucleotides within a sequence for single-nucleotide mapping.
• Model Fitting: Applies mathematical models to fit band intensity profiles for quantitative measurement.
• Band Intensity Normalization: Normalizes band intensities across lanes and experiments to enable comparability.

Scientific Applications:

• Hydroxyl Radical Footprinting: Quantitative analysis of hydroxyl radical (·OH) footprints for solvent-accessible surface mapping.
• DNA Footprinting: Mapping protein–DNA interactions and binding sites by quantifying protection and cleavage patterns.
• RNA Structure Analysis: Monitoring RNA folding and conformational changes via chemical mapping band intensities.
• Chemical Mapping Studies: Comparative analysis of nucleic acid modifications and probe reactivities across experiments.

Methodology:

Computational steps explicitly include lane identification, gel rectification, assignment of bands to individual nucleotides, mathematical model fitting of band intensities, and band intensity normalization across lanes and experiments.