GOPHER

GOPHER generates capture probes for capture Hi-C (CHC) experiments to enable high-resolution mapping of chromatin interactions and promoter regulatory contacts.

Key Features:

• Flexible Probe Design Strategies: Implements three probe-design strategies—Simple, Simple-Patched, and Extended—that place probes relative to restriction digest fragments and transcription start sites (TSS) to tailor coverage.
• Versatile Targeting: Supports probe design for promoters, GWAS hits, and large blocks of sequence.
• Comprehensive Output Options: Produces output files intended for probe ordering and downstream analyses.

Scientific Applications:

• Promoter interaction mapping: Designs probes for capture Hi-C experiments to map promoter interactions and regulatory element contacts at high resolution.
• Gene regulation and chromatin architecture studies: Enables investigation of gene regulatory mechanisms through high-resolution mapping of chromatin architecture.
• GWAS follow-up: Facilitates targeted capture of genomic regions containing disease-associated variants identified by GWAS for interaction analyses.

Methodology:

Implements three explicit probe-placement heuristics: Simple (one probe at each margin of a single digest overlapping the TSS), Simple-Patched (extends Simple to improve coverage when the TSS is near a digest boundary), and Extended (denser, targeted probe placement for smaller gene sets), and emits output files for probe ordering and downstream analysis.