Hello Samir. Happy to answer your question.

You can use the RBS Calculator @ https://salislab.net/software/design_rbs_calculator to design a synthetic RBS that will increase a protein's expression level. To do this, copy/paste your protein coding sequence into the "Protein CDS" input box. Enter a target translation rate between 1 and 250000. Select your host bacterial organism (E. coli or another). Click submit. The algorithm will design a synthetic RBS that binds to the ribosome with a translation initiation rate close to your target. If you'd like to over-express a protein, you should pick a high target translation rate (e.g. 50000 to 250000). There are many additional options, including specifying constant upstream sequences and adding sequence constraints.

The full documentation is available at https://docs.denovodna.com/docs/rbs-calculator.

We've also developed another algorithm, the Operon Calculator, to express 1 or more proteins at the same time. The algorithm designs all the genetic parts (promoter, RBS, CDS) with several additional design rules to ensure robust expression. That design algorithm is available at https://salislab.net/software/design_operon_calculator.

Howard Salis

hello

Pr. Salis,

thank you so much for your reply.

i tried to use the RBS calculator in design mode and i got the following results in the attached image:

so is it the green sequence?

to use the designed sequence, should i put the whole designed sequence?

another question if possible, the operon calculator is ony possible to use for e.coli? not other organism like bacillus subtilis.

thank you for your help.