CATCH

CATCH detects spatial and combinatorial patterns in Chromatin Immuno Precipitation (ChIP) profiling data to identify protein–DNA binding signatures and chromatin modification patterns.

Key Features:

• Exhaustive alignment: Performs a computationally efficient exhaustive alignment of ChIP profiling signals to align areas of enrichment.
• Hierarchical clustering: Applies hierarchical clustering to aligned profiles to group similar spatial and combinatorial patterns.
• De novo pattern detection: Detects known and novel protein–DNA binding and chromatin modification patterns ab initio without requiring prior site annotations.
• High-resolution pattern detection: Resolves intricate and asymmetric histone and histone modification patterns, including around H2A.Z-enriched sites.

Scientific Applications:

• Exploratory chromatin analysis: Enables investigation of the spatial and combinatorial complexity of chromatin-associated protein binding from ChIP profiling data.
• Epigenetic regulation studies: Facilitates identification of histone modification patterns and post-translational modification signatures relevant to epigenetic regulation and gene expression.
• Pattern discovery: Supports ab initio discovery of novel binding patterns and enrichment signatures in ChIP datasets.

Methodology:

Computational steps comprise exhaustive alignment of ChIP profiling signals and computationally efficient hierarchical clustering of aligned enrichment regions.