Tcbf

Tcbf identifies topologically associating domain (TAD) boundaries across multiple species to enable pan-3D genome analysis of chromatin spatial organization and gene regulation in eukaryotic organisms.

Key Features:

• TAD boundary identification: Detects conserved and species-specific topologically associating domain (TAD) boundaries across multiple species.
• Integration of synteny and homology: Integrates gene synteny blocks and homologous sequences to inform boundary identification.
• Scalability: Processes extensive genome datasets to support large-scale pan-3D genome studies and reduce computational demands.
• Implementation: Implemented using Python and R.
• Comparative genomics focus: Supports analysis of evolutionary conservation and divergence in chromatin architecture.

Scientific Applications:

• Pan-3D genome comparison: Comparative analysis of TAD boundary conservation across species.
• Chromatin architecture research: Investigation of relationships between TAD boundary variation and chromatin spatial organization.
• Gene regulation studies: Exploration of functional implications of conserved or species-specific TAD boundaries for gene expression regulation.

Methodology:

Implemented in Python and R, Tcbf integrates gene synteny blocks and homologous sequences to automate detection of conserved and species-specific TAD boundaries and to process extensive genome datasets efficiently.