SeqMonk

SeqMonk analyzes high-throughput mapped sequence data to visualize and quantify genome-wide DNA methylation, gene expression profiles, and sequence alignments for epigenetic and genomic studies.

Key Features:

• Visualization Capabilities: Provides visualization of DNA methylation patterns, gene expression profiles, and mapped sequence alignments.
• Genome-wide Methylation Analysis: Supports assessment and quantification of genome-wide epigenetic modifications such as DNA methylation.
• Bisulfite NGS Support: Processes bisulfite next-generation sequencing data to derive methylation information.
• Comparative Methylation Analysis: Identifies significant differences in methylation patterns between sample groups (e.g., AID-deficient vs. wild-type).

Scientific Applications:

• Epigenetic Reprogramming Studies: Elucidates DNA demethylation mechanisms in mammalian primordial germ cells (PGCs) and early embryos.
• Study of AID Function: Compares methylation in AID-deficient mouse PGCs at embryonic day 13.5 with wild-type to assess AID's role in methylation erasure.
• Genomic Imprinting and Epimutations: Analyzes erasure of genomic imprints and epimutations during development and restoration of pluripotency.
• Transgenerational Epigenetic Inheritance: Evaluates genome-wide methylation patterns relevant to transgenerational epigenetic inheritance and its limitations.

Methodology:

Processes mapped high-throughput bisulfite next-generation sequencing data to profile genome-wide DNA methylation and detect differential methylation between conditions such as AID-deficient versus wild-type samples.