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Biophysical modeling leads to newly discovered molecular interactions between the ribosome and mRNA at standby sites, and predicts how sequences upstream of the Shine-Dalgarno control translation rate and post-transcriptional regulation.

Espah Borujeni, A., Channarasappa A.S., and Salis H.M., (2013) Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites, Nucleic Acid Research, v41 (21)

Learn the origins of "context effects" between promoters and RBSs, and how structured mRNAs can coax the ribosome into performing regulatory tricks.

RBS Calculator

mRNA Sequence [?]
mRNA Sequence: enter the nucleotide sequence of an mRNA transcript, using A/G/C/T/U. (required)

Organism or (16S rRNA) [?]
Organism or 16S rRNA sequence: choose a bacterial species by typing in the first 3 letters of its name and selecting it from the list. Alternatively, you may enter the last 9 nucleotides of the 16S rRNA, using A/G/C/T/U. (required)
(start typing)

Select a Free Energy Model [?]
Free Energy Model Version: Improved versions of our biophysical models are released once their experimental validation has shown a sufficiently large increase in accuracy.

Version 1.0: the original RBS Calculator free energy model, as described in Nature Biotechnology, 2009. This version employs the NuPACK software suite.

Version 1.1: several improvements were made, including a more accurate calculation of the final state's free energy and a modified ribosome footprint length. These changes are described in Methods in Enzymology, v498, 2011. This version employs the ViennaRNA software suite.

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Have a Question? Our Documentation, Publications, and References may have your answer!
When using these results, please reference H.M Salis, Methods in Enzymology 2011 and H.M. Salis, E.A. Mirsky, C.A. Voigt, Nat. Biotech., 2009
We gratefully acknowledge research funding from the Defense Advanced Research Projects Agency, the National Science Foundation, the Office of Naval Research, and an Amazon AWS Research Grant.
Computational resources are provided by the AWS Elastic Compute Cloud.