TADbit

TADbit analyzes and models three-dimensional chromatin structures from Chromosome Conformation Capture (3C) experiments and derivative protocols to derive interaction matrices and reconstruct 3D genomic domain conformations for studying genome architecture relationships with gene expression and epigenetic states.

Key Features:

• Data processing: Preprocesses sequencing reads from 3C-based experiments and maps them to a reference genome for downstream analysis.
• Interaction data handling: Filters and normalizes chromatin interaction data to produce reliable interaction matrices.
• Interaction matrix analysis: Analyzes interaction matrices to identify significant genomic interactions and structural features.
• 3D modeling: Builds three-dimensional models of selected genomic domains to represent chromatin spatial conformations.
• Structural characterization: Quantifies and characterizes structural properties of 3D models to relate chromosomal architecture with gene expression and epigenetic states.

Scientific Applications:

• Genome architecture and function: Links chromatin three-dimensional organization to gene regulation and epigenetic states by analyzing interaction matrices and 3D models.
• Drosophila domain modeling: Applied to model 50 genomic domains from the fly genome, revealing differential structural features associated with various chromatin compositions.

Methodology:

Computational steps explicitly include preprocessing sequencing reads, mapping to a reference genome, filtering and normalizing interaction data, analyzing interaction matrices, building 3D models of genomic domains, and characterizing those models.