crispr-designer

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.

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.