1.28.6 Design a Synthetic RBS with Constraints

RBS Calculator Tutorial Video

  • The "Design synthetic RBS (with constraints)" task is intended for advanced users (Figure 1.28.6.1).
  • This task allows you to create a de novo ribosome binding site (RBS) for a known CDS while using a constraint sequence of nucleotides and N placeholders. The translation initiation rate (TIR) of the designed RBS can be set to any value between 0 and 5687190 or the maximum possible value.
  • This ability can be used to control the translation level of the chosen CDS while defining the RBS length and sequence.


    Figure 1.28.6.1: "Design synthetic RBS with constraints" task fields.

  • Field descriptions:

    • Pick a task field - Allows you to switch to the required task.
    • Pre sequence field - Enter the sequence upstream of the designed RBS. This optional field improves the accuracy of the predicted TIR value. The pre sequence is especially important for short RBS sequences (less than 35bps) produced by the calculator, as this pre-sequence could interfere with the secondary structure of a short RBS and hence alter the TIR.
    • CDS sequence field - Enter the coding sequence of the protein you wish to receive the translation inititation rate (TIR) for, or use the "Use selection" option to choose a sequence from an existing project in Genome Compiler.
    • RBS Constraints field - Enter the template for the requested RBS including length and sequence using A, T, G, C and N as a place holder. The length of the sequence will determine the RBS length.
    • Target TIR field - Enter a specific requested TIR for the designed RBS or optimize the translation rate by choosing the "Maximum" radio button.
    • Organism field - Choose the relevant prokaryotic organism by selecting from the drop down list or by entering part of the name. This choice will change the rRNA field to the last 9 nucleotides of the 16S rRNA of this organism.