Jupyter Notebook scripts for preparing DNA parts for inclusion in Reclone syntax assemblies or in the Open DNA collection. Three main workflows have been produced:
- Synthesis of protein-coding parts (codon-optimized) (Collab Notebook)
- Input protein sequences and 5′/3′ Reclone tags.
- Pipeline reverse-translates, optimizes, enforces constraints, adds Reclone/BbsI adapters, and outputs order-ready DNA parts.
- Best when you want clean, synthesis-grade CDS parts with early-codon tuning.
- Add syntax overhangs & sites by PCR (Collab Notebook)
- You already have a DNA template and want to append Reclone/BbsI ends via PCR.
- The PCR script generates primer sequences that add the correct Type IIS sites, overhangs, and spacers for cloning---no global re-design or codon optimization.
- Best for quick cloning from an existing plasmid or for small variants.
- Synthesis of non-coding parts (no codon optimization) (Collab Notebook)
- For promoters, RBS/UTRs, linkers, terminators, regulatory elements, etc.
- Takes DNA sequences as-is, adds the appropriate Reclone tags and outer BbsI adapters, checks constraints, and outputs order-ready parts.
- Best when the sequence must be preserved (no translation/codon constraints).
Please add any issues you find to the repository!