search

ipb-halle / GoldenMutagenesisWeb

This repository is used for the development of the GoldenMutagenesis web application
GNU Affero General Public License v3.0
0 stars 1 forks source link

Update server_templates.R #37

Open alexanderisme opened 2 years ago

alexanderisme commented 2 years ago

I added two CDS Entry plasmids as requested in #35 The plasmids are pICH41308 for a CDS1 pAGM1287 for a CDS1ns

Hope someone can check if it is working as it is supposed.

Would it make sense to add all level0 acceptors described in the paper? Engler C, Youles M, Gruetzner R, Ehnert T-M, Werner S, Jones JDG, Patron NJ, Marillonnet S. 2014. A Golden Gate Modular Cloning Toolbox for Plants. ACS Synth Biol 3:839–843. doi:10.1021/sb4001504 Screenshot_20220531_134827

sneumann commented 2 years ago

That's great ! I'll setup a server with your code and come back to you. Yours, Steffen

alexanderisme commented 2 years ago

Dear Steffen, I just noticed that for the "pAGM1287 for CDS1ns" there might be additional tweaks necessary since two base pairs have to be reintroduced in order to get the sequence of the C-Tag in frame again. The "easy" solution would be to force a longer 3' overhang and use eg tcTTCG (reverse complemented = CGAAGA). The elegant way would be to check if the sequence has or can be changed to a silent mutation introducing a T at the end of the sequence... But that would require more code and I am not able to do that.

Possibly the pAGM1287 for CDS1ns can be taken out for the moment in order to avoid confusion...

sneumann commented 2 years ago

Hi, thanks for your #37, which already addresses the difficult parts! I only had to add that choice to the web interface. That version is now available for testing in https://msbi.ipb-halle.de/GoldenMutagenesisWebDevel/ Could you please test-drive that ? Yours, Steffen

alexanderisme commented 2 years ago

Wonderful, everything looks perfect to me. Thank you very much!

sneumann commented 2 years ago

Does that also include I magically fixed #34 ? Yours, Steffen

alexanderisme commented 2 years ago

No, sadly that much magic happens only in Christmas time :smile: I was only referring to the overhangs formed by the pICH41308 vector...