BiQ Analyzer HiMod

BiQ Analyzer HiMod performs high-throughput locus-specific analysis of DNA cytosine modifications, quantifying 5-methylcytosine (5mC) and its oxidized derivatives such as hydroxymethylation, formylation, and carboxylation from sequence data.

Key Features:

• Sequence alignment and quality control: Performs sequence alignment and quality control on raw sequence reads to prepare data for modification calling.
• DNA modification statistics: Calculates locus-specific DNA modification statistics for 5mC and its oxidized derivatives.
• Support for multiple assay types: Supports four distinct assay types for profiling methylation and oxidative cytosine modifications.
• Custom vector graphics engine: Generates publication-quality vector graphics for visualization of DNA modification patterns.
• Support for multiple data formats: Accepts and outputs multiple input and output data formats to accommodate diverse datasets.
• End-to-end processing: Provides a workflow from raw sequence data to computed DNA modification statistics and visualizations.

Scientific Applications:

• Epigenetic profiling: Locus-specific profiling of 5mC and oxidized cytosine derivatives in targeted or high-throughput experiments.
• Gene regulation and development: Investigation of relationships between DNA modification patterns and gene regulation or developmental processes.
• Disease mechanism studies: Analysis of methylation and oxidative modification changes relevant to disease mechanisms.

Methodology:

Implements sequence alignment and quality control, computes locus-specific DNA modification statistics, and produces vector graphics for visualization.