Primer design endpoints

[manulera]

POST /primer_design/whatever?options -> submit sequences

TODO:

• [x] Add tests
• [ ] Add Gibson functionality:
  • [ ] This should allow for the user to specify which fragments you want to amplify with tails and which not.
  • [ ] In the frontend, there should be some representation
  • [ ] There should be possible to specify which subfragment you want to amplify, or join the entire fragment.
• [ ] Add restriction-ligation primer functionality (for res-lig cloning)

[manulera]

Tests are missing

https://github.com/manulera/ShareYourCloning_backend/pull/142

[manulera]

By the way @dgruano could you upload a photo with the drawing of the type of Gibson that you mentioned yesterday? Just to be sure that I understand 100%

[dgruano]

Here it is!

For Gibson Assembly you need a minimum homology region between fragments, and we would usually achieve this by adding homology tails through PCR (e.g. Option 1). We can add tails to different fragments, and still get the Gibson to work (e.g. Option 2). That also means that we don't necessarily need to add homology tails to every single fragment (e.g. Option 3). Note that all options drawn here have the required homology for Gibson assembly.

In the context of SYC, a user designing oligos for their Gibson assembly may decide to add the minimum amount of recombination tails, as well as to which fragments they are added.

[dgruano]

For the record, NEB's guide for Gibson Assembly design suggests to design overlapping primers (Figure 2A and 2B, page 4) 🤷‍♂️.