DMEAS

DMEAS quantifies DNA methylation patterns and evaluates epigenetic heterogeneity from bisulfite sequencing data at locus-specific and genome-wide scales.

Key Features:

• Progressive scanning: Examines mapping results from bisulfite sequencing reads using a progressive scanning mechanism to extract contiguous CpG dinucleotide methylation patterns.
• Methylation level estimation: Determines DNA methylation levels from extracted read-level patterns.
• Methylation entropy calculation: Calculates methylation entropy as a quantitative metric of pattern complexity and variability.
• Epigenetic heterogeneity assessment: Quantifies variability of DNA methylation within cell populations across genomic segments.
• Multi-sample comparison: Enables comparative analysis of methylation patterns between multiple samples or conditions.
• Locus-specific and genome-wide analysis: Supports analysis focused on specific loci as well as genome-wide datasets from bisulfite sequencing.

Scientific Applications:

• Cancer biology: Quantifies methylation heterogeneity and pattern complexity in cancer-related studies.
• Developmental biology and differentiation: Assesses DNA methylation dynamics during development and cellular differentiation.
• Epigenetic biomarker discovery: Identifies methylation patterns and markers associated with specific phenotypes or pathologies.
• Comparative methylation studies: Detects differences in methylation patterns across samples or experimental conditions.

Methodology:

DMEAS applies a progressive scanning algorithm to mapping results from bisulfite sequencing reads to extract methylation patterns across contiguous CpG dinucleotides, estimates methylation levels, computes methylation entropy, and performs multi-sample comparisons for locus-specific and genome-wide analyses.