By 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.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command
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
- Identify Target Locus:
- Resolve the gene name to the current reference genome (GRCh38 for humans).
- Identify functional domains (exons) that are constitutively expressed.
- Design gRNAs:
- Select 20nt targets adjacent to NGG PAM sites.
- Prioritize 5' constitutive exons for knockouts to ensure early truncation.
- 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.
- Output Table:
- Return a markdown table with: Sequence, PAM, On-Target Score, Off-Target Score, and Genomic Location.
- Recommend the top 3 guides.