CaptureProbe

CaptureProbe designs capture probes for Capture Hi-C to enable targeted interrogation of chromatin interactions and non-coding regulatory regions.

Key Features:

• Implementation: Implemented in Java for probe design computations.
• Capture Hi-C compatibility: Designs probes specifically for Capture Hi-C using hybridization capture technology.
• Parameter customization: Provides extensive parameter customization to optimize probe design for experimental needs.
• Targeted design: Generates probes for individual genomic sites and broader genomic regions.
• Probe optimization and specificity: Optimizes design parameters to improve capture success and reports superior probe specificity compared with HiCapTools and GOPHER.

Scientific Applications:

• Chromatin interaction mapping: Enables targeted identification of interactions between target loci and other genomic regions using Capture Hi-C.
• Chromatin architecture and gene regulation: Facilitates investigation of chromatin looping and folding and their roles in gene regulation.
• Non-coding regulatory element analysis: Supports analysis of non-coding regions implicated in traits and diseases.

Methodology:

Implements probe design and parameter optimization for Capture Hi-C hybridization capture; implemented in Java.