1.28.3 Reverse Engineer mRNA Sequence

RBS Calculator Tutorial Video

  • The "Reverse engineer mRNA sequence" task enables you to identify all possible ribosome binding sites (RBS) in a sequence (Figure 1.28.3.1).
  • This ability can be used to find all possible ORFs in a prokaryotic mRNA sequence by calculating the TIR of each or to check the TIR of a CDS starting at the first ATG codon.


    Figure 1.28.3.1: "Reverse engineering of mRNA sequence" task fields.

  • Field Descriptions:
    • Pick a task field - Allows you to switch to the required task.
    • mRNA sequence field - Input the mRNA sequence you wish to analyze or use the "Use selection" option to choose a sequence from an existing project in Genome Compiler.
    • Only check the first ATG/AUG field - Using this option will limit the RBS calculation to the first ATG in the sequence which will make the calculation faster. If this option is not selected the RBS calculator will run for all possible prokaryotic start codons (AUG, GUG, UUG, CUG).
    • 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.