1.28.2 Choosing the Desired RBS Mode
The RBS Calculator main page will open as a new project sub tab where the four RBS tasks are listed (Figure 18.104.22.168).
In this page you can choose the relevant RBS task:
- Reverse engineer mRNA sequence - Use this option when you have an mRNA sequence that you want to analyse. It will predict possible RBS sequences and their TIRs for all possible prokaryotic start codons or for the first ATG codon in an mRNA sequence. This mode can therefore help to predict the most translated coding sequence.
- Analyze a RBS - Use this option when you know the RBS and its corresponding coding sequence and you want to predict the translation initiation rate (TIR) of the RBS for a particular CDS (50bp+) and decide if you need to optimise it.
- Design synthetic RBS - Use this option to optimise the translation rate for your coding sequence, by designing a novel RBS according to a user-defined translation initiation rate (TIR) or the maximum TIR possible for a given CDS.
Design synthetic RBS with constraints - Intended for advanced users. Use this option to design a novel RBS sequence like in the previous option, but also add constraints based on a given sequence of nucleotides (accepts A, T, G, C and N) for example to include a restriction site or primer binding site within or nearby the RBS.
See each of the following individual sections to understand in more detail how to use each mode.