Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-genome-engineering-hdr-template-design

Maintainer FreedomIntelligence · Last updated April 1, 2026

Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.

OpenClawNanoClawAnalysisReproductionbio-genome-engineering-hdr-template-design🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epidemiological & causal genomicsdesign

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-engineering-hdr-template-design

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: primer3.bindings.design_primers() (primer3-py) for primer/arm design, Bio.Seq for template construction.
Design a donor template for my CRISPR knock-in" → Create homology-directed repair templates (ssODN, dsDNA, or plasmid) with optimized homology arm lengths and silent PAM mutations, using primer3 for flanking primer design. Python: primer3.bindings.design_primers() (primer3-py) for primer/arm design, Bio.Seq for template construction.
TAGS = { 'FLAG': 'GATTACAAGGATGACGATGACAAG', '3xFLAG': 'GATTACAAGGATGACGATGACAAGGATTACAAGGATGACGATGACAAGGATTACAAGGATGACGATGACAAG', 'HA': 'TACCCATACGATGTTCCAGATTACGCT', 'V5': 'GGTAAGCCTATCCCTAACCCTCTCCTCGGTCTCGATTCTACG', 'MYC': 'GAACAAAAACTCATCTCAGAAGAGGATCTG', '6xHIS': 'CATCACCATCACCATCAC', 'GFP_LINKER': 'GGCGGAGGCGGAAGC', # Flexible linker before GFP }.
def design_tag_insertion(target_seq, cut_site, tag_name, position='C-term'): '''Design HDR donor for protein tagging.
Args: position: 'N-term' or 'C-term' relative to target gene.

Source Doc

Excerpt From SKILL.md

dsDNA Donor Design

Goal: Design a double-stranded DNA donor template with long homology arms for larger CRISPR knock-in insertions, along with PCR primers for amplification.

Approach: Extract left and right homology arms of specified length flanking the cut site, concatenate with the insert sequence, then design PCR primers for the arms and Gibson assembly overlap primers that span the arm-insert junctions.

Use cases

Use when designing donor templates for precise insertions, tagging, or allele replacement.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

genome-engineering/grna-design - Design guide to create cut site
primer-design/primer-basics - PCR primer design for cloning
sequence-io/read-sequences - Read and parse GenBank features

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