How do I install the Crispr Sgrna Designer skill?

Run npx skillmds@latest add dvcrn/crispr-sgrna-designer in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Crispr Sgrna Designer safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Crispr Sgrna Designer?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Crispr Sgrna Designer free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Crispr Sgrna Designer?

dvcrn (@dvcrn) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Crispr Sgrna Designer by dvcrn — Agent Skill

Name: Crispr Sgrna Designer
Rating: 4.2 (5 reviews)
Author: dvcrn

Crispr Sgrna Designer

Professional-grade CRISPR sgRNA design for viral and microbial genomes, with specialized logic for extreme-GC templates (e.g., Herpesviruses). Use when needing to design high-efficiency, low-off-target sgRNAs for (1) Gene knockouts, (2) Site-specific insertions/tagging, or (3) Precise genome editing. Includes PAM scanning, position-weight scoring (Rule Set 2 style), and synonymous mutation strategy for donor template design. Designed by ZJU PhD @ Bio-chat.

dvcrn Updated Sep 8, 2026 32 repo stars

File contents

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

---name: crispr-sgrna-designerdescription: Professional-grade CRISPR sgRNA design for viral and microbial genomes, with specialized logic for extreme-GC templates (e.g., Herpesviruses). Use when needing to design high-efficiency, low-off-target sgRNAs for (1) Gene knockouts, (2) Site-specific insertions/tagging, or (3) Precise genome editing. Includes PAM scanning, position-weight scoring (Rule Set 2 style), and synonymous mutation strategy for donor template design. Designed by ZJU PhD @ Bio-chat.---# 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 Capabilities1. **Precision PAM Scanning**: Automated scanning of target regions for SpCas9 (NGG) and alternative PAMs.2. **GC-Weighted Scoring**: Specialized weighting for high-GC templates (65-80% GC) to ensure thermodynamic stability of the R-loop.3. **Positional Analysis**: Calculates cut sites relative to functional features (ATG start codons, stop codons, or exon junctions).4. **Off-target Defense**: Rapid genomic indexing to ensure seed-region (12bp) uniqueness in small viral/microbial genomes.5. **Donor Template Strategy**: Automatically suggests synonymous mutations to prevent re-cutting of integrated donor sequences.## Workflow1. **Target Identification**: Provide a genomic region or gene name (e.g., PRV UL15 N-terminus).2. **Sequence Extraction**: Automatically pulls the latest reference sequences via NCBI E-utils.3. **sgRNA Generation**: Runs a sliding window scan for NGG PAMs within the target window.4. **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.5. **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*

Frequently asked questions