A professional-grade CRISPR sgRNA design tool optimized for high-GC viral and microbial genomes with specialized scoring and off-target analysis.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install crispr-sgrna-designer
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install crispr-sgrna-designer using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is CRISPR sgRNA Designer?
The CRISPR sgRNA Designer is a specialized skill within the Openclaw Skills ecosystem designed for precision genome engineering. While standard design tools often fail in extreme sequence contexts, this skill features specialized logic for extreme-GC templates (65-80% GC), such as those found in Herpesviruses. It provides researchers and developers with a rigorous framework for identifying high-efficiency, low-off-target sgRNAs for Cas9-mediated gene knockouts and site-specific insertions.
Developed by ZJU PhD experts, this tool integrates position-weight scoring and synonymous mutation strategies directly into the design workflow. By leveraging Openclaw Skills, users can automate the complex transition from genomic sequence extraction to experimental-ready donor template design, ensuring thermodynamic stability and high specificity in the R-loop formation.
CRISPR sgRNA Designer Use Cases
- Designing high-efficiency sgRNAs for viral gene knockouts in high-GC genomes.
- Creating donor templates with synonymous mutations to prevent Cas9 re-cutting.
- Site-specific protein tagging or genomic insertions in microbial systems.
- Precise genome editing requiring SpCas9 (NGG) PAM scanning and 12bp seed region uniqueness.
How CRISPR sgRNA Designer Works
- Target Identification: The user specifies a genomic region or gene name, such as the PRV UL15 N-terminus.
- Sequence Extraction: The system automatically retrieves the latest reference sequences using NCBI E-utils.
- sgRNA Generation: A sliding window scan is performed to locate all possible NGG PAM sites within the target window.
- On-target Scoring: Each candidate is scored using modified Rule Set 2 logic, applying specific rewards for seed-region nucleotides and penalties/rewards for GC content.
- Off-target Defense: The tool performs a genomic index check to ensure 12bp seed-region uniqueness.
- Result Ranking: A prioritized list of candidates is generated with scores from 0-100 and experimental recommendations.
CRISPR sgRNA Designer Setup
To integrate this skill into your workflow, ensure your environment has access to the Openclaw Skills framework and NCBI E-utils. Use the following command to initialize the designer:
# Install the CRISPR sgRNA Designer skill
claw install crispr-sgrna-designer
# Configure NCBI API Key (optional for higher rate limits)
export NCBI_API_KEY='your_key_here'
CRISPR sgRNA Designer Data Schema & Taxonomy
The CRISPR sgRNA Designer organizes output data into a structured format for downstream wet-lab applications:
| Attribute | Description |
|---|---|
| sgRNA Sequence | 20nt sequence excluding the PAM. |
| PAM | The 3nt Protospacer Adjacent Motif (NGG). |
| Score (0-100) | The composite efficiency score based on Rule Set 2. |
| GC Content | Percentage of G/C bases, optimized for viral templates. |
| Position | The specific genomic coordinate of the cut site. |
| Synonymous Mutation | Suggested changes for donor template design. |
CRISPR sgRNA Designer Advanced Features
- Extreme-GC Optimization: Tailored weighting for templates with 65-80% GC content.
- Multi-PAM Support: Extensible scanning for alternative PAM sequences beyond SpCas9.
- Donor Template Strategy: Automatic calculation of synonymous mutations for seamless homology-directed repair (HDR) planning.
- Automated Reference Fetching: Direct integration with NCBI for real-time sequence updates.
SKILL.md
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