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molecular-cloning

Molecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design, CRISPR sgRNA design, and plasmid annotation. For protein-level sequence analysis use biopython or esm; for database lookups use gene-database or ensembl-database.

backend/cli/skills/biology/molecular-cloning/SKILL.md

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# Molecular Cloning: Sequence Engineering & Cloning Design

## Overview

Molecular Cloning provides computational tools for simulating and designing molecular cloning workflows. This skill covers PCR amplicon prediction with primer binding analysis, restriction enzyme digestion simulation, Golden Gate and Gibson assembly design and verification, primer design with thermodynamic calculations, CRISPR sgRNA design with off-target scoring, and plasmid feature annotation. All simulations use Biopython's Bio.Restriction and Bio.SeqUtils for accurate enzyme and sequence handling.

## When to Use This Skill

- Predicting PCR amplicons from primer sequences and templates
- Simulating restriction enzyme digestions and predicting fragment sizes
- Designing Golden Gate assembly with 4bp overhang compatibility
- Planning Gibson assembly with overlap design
- Designing PCR primers with Tm and specificity constraints
- Designing CRISPR sgRNAs and scoring off-target potential