Designs guide RNA (gRNA) sequences for CRISPR-Cas9 editing, including off-target analysis. Use when a user needs to edit a gene or asks for gRNA sequences.
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---name: crispr-designer
description: Designs guide RNA (gRNA) sequences for CRISPR-Cas9 editing, including off-target analysis. Use when a user needs to edit a gene or asks for gRNA sequences.
keywords:
- crispr-designer
- automation
- biomedical
measurable_outcome: execute task with >95% success rate.
---"
# CRISPR gRNA Designer
This skill designs high-efficiency guide RNAs for gene editing experiments.
## When to use this skill
- When a user provides a gene name (e.g., "TP53"), Ensembl ID, or DNA sequence.
- When the user wants to perform "knockout", "activation" (CRISPRa), or "interference" (CRISPRi).
- When specificity and off-target minimization are requested.
## How to use it
1. **Identify Target Locus:**
- Resolve the gene name to the current reference genome (GRCh38 for humans).
- Identify functional domains (exons) that are constitutively expressed.
2. **Design gRNAs:**
- Select 20nt targets adjacent to NGG PAM sites.
- Prioritize 5' constitutive exons for knockouts to ensure early truncation.
3. **Score Candidates:**
- Calculate **On-Target Efficiency** (e.g., Rule Set 2 score).
- Calculate **Off-Target Specificity** (CFD score) by searching the whole genome for mismatches.
4. **Output Table:**
- Return a markdown table with: Sequence, PAM, On-Target Score, Off-Target Score, and Genomic Location.
- Recommend the top 3 guides.
