ABSP

ABSP analyzes region-specific CpG methylation from bisulfite sequencing PCR (.ab1) data to compute methylation percentages for epigenetic studies.

Key Features:

• R-based implementation: Implemented in R for computational analysis of bisulfite sequencing PCR data.
• Supported BSP methodologies: Supports both direct-BSP and cloning-BSP approaches for region-specific bisulfite sequencing.
• Raw trace file processing: Processes raw sequencing trace files (.ab1) derived from bisulfite-treated DNA.
• Methylation quantification: Computes CpG methylation percentages and distinguishes methylated from unmethylated cytosines.
• Quality control integration: Integrates quality control checks to ensure reliability and accuracy of methylation percentage calculations.
• Automated workflow: Automates analysis steps including data input, quality control, analysis, and visualization.
• Publication-ready outputs: Generates publication-quality graphics and comprehensive reports.

Scientific Applications:

• Epigenetic research: Enables precise quantification of CpG methylation to study epigenetic gene regulation across contexts such as embryonic development, cancer, and neurodegenerative disorders.
• Cancer studies: Facilitates identification of aberrant methylation patterns that may serve as biomarkers or therapeutic targets in oncology research.
• Neurodegenerative disorders: Supports investigation of epigenetic changes associated with neurodegenerative disease mechanisms.

Methodology:

Processes raw .ab1 sequencing trace files to compute CpG methylation percentages from bisulfite-treated DNA, employs robust algorithms to distinguish methylated and unmethylated cytosines, and executes an automated workflow comprising data input, quality control checks, analysis, visualization, and report generation.