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/install crispr-sgrna-designer
Description
Professional-grade CRISPR sgRNA design for viral and microbial genomes, with specialized logic for extreme-GC templates (e.g., Herpesviruses). Use when needi...
README (SKILL.md)
CRISPR sgRNA Designer (Bio-chat Series)
This skill provides a rigorous workflow for designing and scoring CRISPR/Cas9 sgRNAs, specifically optimized for high-GC viral genomes where standard tools often struggle.
Key Capabilities
- Precision PAM Scanning: Automated scanning of target regions for SpCas9 (NGG) and alternative PAMs.
- GC-Weighted Scoring: Specialized weighting for high-GC templates (65-80% GC) to ensure thermodynamic stability of the R-loop.
- Positional Analysis: Calculates cut sites relative to functional features (ATG start codons, stop codons, or exon junctions).
- Off-target Defense: Rapid genomic indexing to ensure seed-region (12bp) uniqueness in small viral/microbial genomes.
- Donor Template Strategy: Automatically suggests synonymous mutations to prevent re-cutting of integrated donor sequences.
Workflow
- Target Identification: Provide a genomic region or gene name (e.g., PRV UL15 N-terminus).
- Sequence Extraction: Automatically pulls the latest reference sequences via NCBI E-utils.
- sgRNA Generation: Runs a sliding window scan for NGG PAMs within the target window.
- On-target Scoring:
- Position Weighting: Rewards specific nucleotides in the seed region.
- GC Penalty/Reward: Optimizes for the high-GC context of viruses like PRV.
- Result Ranking: Provides a ranked list of sgRNAs with comprehensive scoring (0-100) and experimental recommendations.
Technical Standards
- Scoring Model: Modified Rule Set 2 logic adapted for extreme sequence contexts.
- Seed Region: Strict 12bp specificity check.
- PAM Requirement: 5'-NGG-3' (Standard SpCas9).
Designed by ZJU PhD @ Bio-chat Community
Usage Guidance
This skill appears coherent with its stated purpose: it fetches sequences from NCBI and scores candidate sgRNAs. Before installing, note: (1) the bundled Python script requires the requests and Biopython packages which are not listed in the metadata—ensure those are installed in a controlled environment; (2) the script will make network requests to NCBI (efetch); confirm this is allowed from your environment and consider NCBI rate limits and privacy of sequences you submit; (3) inspect and run the script on non-sensitive test sequences first to validate behavior; and (4) if you plan autonomous agent invocation, be aware outputs (designed guides) may be generated automatically—ensure that is acceptable for your workflow. If you need higher assurance, request explicit dependency declarations and a maintainer/homepage for provenance.
Capability Analysis
Type: OpenClaw Skill
Name: crispr-sgrna-designer
Version: 0.1.0
The skill provides a legitimate tool for CRISPR sgRNA design, specifically optimized for high-GC viral genomes. The Python script (scripts/design_sgrna.py) fetches sequence data from the official NCBI E-utils API and performs local sequence analysis using standard libraries like Biopython. There are no indicators of data exfiltration, malicious execution, or prompt injection; all behaviors are consistent with the stated scientific purpose.
Capability Assessment
Purpose & Capability
The name/description align with the included script: PAM scanning (NGG), scoring heuristics, reverse-complement scanning, and NCBI E-utilities fetching are implemented. Minor mismatch: the package requires Python libraries (requests, Biopython) but the skill metadata lists no dependencies—this is an engineering omission, not obviously malicious.
Instruction Scope
SKILL.md instructs the agent to fetch reference sequences from NCBI and score candidate guides; the script performs exactly those network calls and local sequence processing and does not read unrelated system files or transmit data to other endpoints.
Install Mechanism
There is no install spec (instruction-only), which minimizes risk, but the bundled Python script requires third-party packages (requests, Biopython) that are not declared—users or the runtime will need to install these before execution.
Credentials
The skill does not request any environment variables, credentials, or config paths. The script makes only outbound HTTP calls to NCBI, which matches the declared functionality.
Persistence & Privilege
The skill is not always-enabled and uses default autonomous invocation settings. It does not attempt to modify other skills or system-wide agent settings.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install crispr-sgrna-designer - After installation, invoke the skill by name or use
/crispr-sgrna-designer - Provide required inputs per the skill's parameter spec and get structured output
Version History
v0.1.0
Initial release of crispr-sgrna-designer for precise CRISPR sgRNA design in viral/microbial genomes, especially high-GC templates.
- Scans target regions for SpCas9 PAMs (NGG and alternatives) with precision.
- Scores sgRNA candidates using specialized high-GC weighting and modified Rule Set 2 positional logic.
- Ensures seed-region (12bp) uniqueness to minimize off-target effects.
- Automatically suggests synonymous donor mutations to prevent re-cutting.
- Fetches latest genomic references from NCBI for each design session.
Metadata
Frequently Asked Questions
What is CRISPIR sgRNA Designer?
Professional-grade CRISPR sgRNA design for viral and microbial genomes, with specialized logic for extreme-GC templates (e.g., Herpesviruses). Use when needi... It is an AI Agent Skill for Claude Code / OpenClaw, with 248 downloads so far.
How do I install CRISPIR sgRNA Designer?
Run "/install crispr-sgrna-designer" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is CRISPIR sgRNA Designer free?
Yes, CRISPIR sgRNA Designer is completely free, licensed under MIT-0. You can download, install and use it at no cost.
Which platforms does CRISPIR sgRNA Designer support?
CRISPIR sgRNA Designer is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created CRISPIR sgRNA Designer?
It is built and maintained by zjuphD (@zjuphd); the current version is v0.1.0.
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