AR
Data & Repro
arxiv-database
This skill provides Python tools for searching and retrieving preprints from arXiv.org via its public Atom API. It supports keyword search,…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-genome-engineering-prime-editing-design
Maintainer FreedomIntelligence · Last updated April 1, 2026
Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-engineering-prime-editing-design
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: PrimeDesign algorithms with Bio.Seq for sequence handling.
- Design a prime editing guide for my point mutation" → Generate pegRNA sequences (spacer, scaffold, RT template, PBS) for precise genomic modifications without double-strand breaks, optimizing PBS length and RT template for editing efficiency. Python: PrimeDesign algorithms with Bio.Seq for sequence handling.
- CAS9_SCAFFOLD = 'GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC.
- def assemble_pegrna(spacer, scaffold, rt_template, pbs): '''Assemble full pegRNA sequence for ordering.
- Components in 5' to 3' order: 1. Spacer (20nt) 2. Scaffold (~76nt for SpCas9) 3. RT template (variable) 4. PBS (13-17nt).
Source Doc
Excerpt From SKILL.md
PE3 Nicking Guide Design
Goal: Design a second nicking guide for the PE3 prime editing strategy to improve editing efficiency by nicking the non-edited strand.
Approach: Search for PAM sites 40-100bp from the pegRNA nick site on the opposite strand, score candidates by proximity to the optimal 50-80bp distance, and return ranked options.
Use cases
- Use when designing prime editing experiments for precise insertions, deletions, or point mutations.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- genome-engineering/grna-design - Standard guide design for comparison
- genome-engineering/base-editing-design - Alternative for C/G to T/A changes
- variant-calling/variant-annotation - Identify pathogenic variants to correct
Related skills
Related skills
BA
Data & Repro
bayesian-optimizer
Bayesian optimization for experimental design and hyperparameter tuning in biomedical research.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-files-bam-statistics
Compute alignment statistics: flagstat, idxstats, coverage depth.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-msa-statistics
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when com…
FreedomIntelligence/OpenClaw-Medical-SkillsView