# Crispr Design Agent

> A specialized tool for designing efficient and specific gRNA sequences for CRISPR-Cas9 experiments.

- Skill: `majiayu000/crispr-design-agent-2` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add majiayu000/crispr-design-agent-2`
- Raw SKILL.md: https://api.skillmd.com/api/skills/majiayu000/crispr-design-agent-2/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- License: MIT
- Author: majiayu000 (https://skillmd.com/u/majiayu000)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/majiayu000/crispr-design-agent-2

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# CRISPR Design Agent

The **CRISPR Design Agent** automates the selection of guide RNAs (gRNAs) for gene editing. It scans DNA sequences for PAM sites, extracts spacers, and scores them based on efficiency rules (GC content, homopolymers).

## When to Use This Skill

*   When designing a CRISPR knockout or knock-in experiment.
*   To find all valid Cas9 target sites in a given DNA sequence.
*   To filter gRNAs by efficiency scores.

## Core Capabilities

1.  **Target Discovery**: Identifies NGG PAM sites.
2.  **Efficiency Scoring**: Calculates scores based on GC content and sequence features.
3.  **Filtering**: Sorts guides by predicted efficacy.

## Workflow

1.  **Input**: Provide a DNA sequence (raw string or FASTA file) and target gene name.
2.  **Process**: The agent scans the sequence and applies scoring logic.
3.  **Output**: Returns a ranked list of gRNA sequences with coordinates and scores.

## Example Usage

**User**: "Find gRNAs for this sequence: ATCG..."

**Agent Action**:
```bash
python3 Skills/Genomics/CRISPR_Design_Agent/crispr_designer.py \
    --sequence "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTGTGAGTGGATCCATTGGAAGGGC" \
    --output guides.json
```