HMST-Seq-Analyzer

HMST-Seq-Analyzer analyzes DNA methylation (5mC) and hydroxymethylation (5hmC) sequencing data to detect, quantify, and annotate differential methylation and hydroxymethylation at single-base resolution.

Key Features:

• Simultaneous detection: Processes Hydroxymethylation-and Methylation-Sensitive Tag sequencing (HMST-seq) data to detect 5mC and 5hmC at single base-pair resolution.
• Differential analysis: Performs differential methylation analysis and identifies Differentially Methylated Regions (DMRs) with genomic annotation.
• Data compatibility: Accepts HMST-seq, whole-genome bisulfite sequencing (WGBS), and reduced representation bisulfite sequencing (RRBS) datasets.
• Visualization and quality control: Produces visual summaries of methylation status and performs preliminary quality checks.
• Computational performance: Implemented in Python and supports parallel processing for large datasets.

Scientific Applications:

• Epigenetic profiling: Enables exploration of 5mC and 5hmC distributions and their roles in gene regulation.
• Developmental biology: Supports analysis of methylation and hydroxymethylation dynamics across developmental stages.
• Disease and cancer research: Identifies methylation and hydroxymethylation changes associated with disease processes such as cancer.

Methodology:

Analyzes HMST-seq (Hydroxymethylation-and Methylation-Sensitive Tag sequencing) and accepts WGBS and RRBS inputs; performs differential methylation analysis to identify DMRs with annotation, provides visualization and preliminary quality checks, and is implemented in Python with parallel processing.