What scripts are you using for DNA synthesis prep? (codons, domestication, syntax, RE cut sites)

Nucleus
1

Hi All

I’d love that it becomes much easier for people to design new parts of the Open DNA Collections and we all know that much of this can be automated (and has been) but we need to converge on a recommended (set of) solution(s) for the community.

It would be great to know:

  1. What are the existing software tools you are using or would recommend? (e.g. primer3 for primer design; OpenCloning from @manulera)
  2. Do any of you have scripts for codon optimization, checking for restriction enzyme sites, primer design, etc? Can you point to GitHub repos, google collab notebooks?
  3. What would your preference be for Reclone to provide/recommend: a) well-documented scripts on a colab/Jupyter Hub (i.e. you copy and paste/upload sequences and click go); b) a GUI-based option; c) Both; d) Other.

Please add your thoughts to the thread below so we can gather existing solutions and figure out the gaps and how to host these tools for the community (mostly likely via an existing solution/organisation).

Thanks so much for your time and suggestions!

Jenny

2

Going to tag @osn_scott into this as his colleague Ian C helped write a script to add in the appropriate pTI- and SEVA-compatible Reclone syntax overhangs when we were designing the Open DNA Collections (Phase 2) wishlist.
Do you know if Ian would be happy to share the scripts he made for this?

This may fall into a slightly different discussion point but, as you know, the current Open DNA Collections (Phase 1) are documented on our GitHub - Reclone-org/Open-DNA-Collections, which is our current main source of information on the available parts. It’ll be useful to hear if you use this repo, and we welcome suggestions on how best to make this tool accessible to the community, any issues with it, and give feedback on parts that have been used. Thank you!

3

Ian C and I have been using DNA Chisel, part of the software suite of the Edinburgh Genome Foundry, with BioPython for sequence optimization - very useful for codon optimization, ensuring specific restriction sites are removed, etc. We used it to assemble all of the Reclone wishlist raw sequences as parts and export a well annotated genbank file.
https://edinburgh-genome-foundry.github.io/DnaChisel/
The Foundry’s github has a lot of other useful tools.
https://edinburgh-genome-foundry.github.io/

Biopython can import Entrez for access to NCBI resources.

Not a real python programmer (like me)? I recently used Google’s Gemini AI to write some scripts to update SNP data from GRCH37 (standard for Genome Wide Association Studies) to GRCH38 reference so I could check my whole genome sequences. Had to do a bit of trouble shooting but with a bit of back and forth feeding in the error message I got the script working. Some AI are getting better and better at writing code hence the labour downsizing of many software companies.

I love OpenCloning.org and am excited that @manulera and team are adding in persistence. I would love to have an OpenCloning site that has all of the Open Yeast and Yeast Protein Expression Toolkit parts as select-able options for a Golden Gate Assembly.

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