CHOPCHOP

CHOPCHOP is a web-based tool for identifying optimal CRISPR-Cas single guide RNA (sgRNA) target sites. Given a target gene, genomic sequence, or chromosome coordinates, CHOPCHOP scores and ranks potential target sites using current algorithms. The tool is managed by ELIXIR Norway and is intended for researchers working with CRISPR-based genome editing who need to identify and evaluate candidate guide RNA targets.

CHOPCHOP runs entirely in the browser with no software installation required. Users select an organism and CRISPR mode, enter a target gene name, genomic sequence, or chromosome coordinates, and receive a ranked list of sgRNA candidates ready for experimental design.

Supported Targeting Systems

• Cas9
• Cpf1
• TALEN

Key Features and Capabilities

• Flexible input: accepts gene names, genomic sequences, or chromosome coordinates across a range of organisms
• Ranked results: candidate target sites are scored and ranked based on predicted efficiency and specificity
• Configurable parameters: a default mode provides quick results, while an advanced mode allows fine-tuned control over scoring and filtering options
• Web-based access: no local installation is needed; the tool runs fully in the browser

Workflow

1. Navigate to the CHOPCHOP web interface
2. Select the target organism and CRISPR system (Cas9, Cpf1, or TALEN)
3. Enter the target gene name, genomic sequence, or chromosome coordinates
4. Review the ranked sgRNA candidates and apply any advanced filtering as needed
5. Use the results to inform experimental guide RNA design

CHOPCHOP is managed by ELIXIR Norway as part of its portfolio of bioinformatics services, providing a maintained and accessible resource for CRISPR target identification.