C-InterSecture

C-InterSecture performs interspecies comparisons of 3D genome architecture using Hi-C map data to liftover chromosomal contacts and quantify contact patterns for evolutionary analysis.

Key Features:

• Liftover Contacts Between Species: Performs liftover of chromosomal contacts between species to enable cross-species mapping of Hi-C interactions.
• 3D Organization Comparison: Compares the three-dimensional organization of defined genomic regions, such as topologically associated domains (TADs).
• Statistical Analysis of Contact Frequencies: Provides statistical analysis of individual contact frequencies between loci.
• Interspecies Comparison of Contact Patterns: Compares contact patterns within specific genomic regions across species to assess how changes in genomic distance affect 3D genome architecture.

Scientific Applications:

• Comparative vertebrate genome architecture: Applied to compare genome organization between mammals and avian species and to investigate evolutionary impacts of genomic distance on 3D genome configuration.

Methodology:

The pipeline operates on Hi-C map data and is implemented as a collection of Python scripts; it performs liftover of chromosomal contacts, conducts statistical analysis of contact frequencies between loci, and generates Jucebox-compatible .hic files.