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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

Pre-Sequence [?]
Pre-Sequence: enter a nucleotide sequence (5 to 20 bp) that appears before the ribosome binding site, using A/G/C/T/U. The Pre-Sequence is important when the ribosome binding site is less than 35 nucleotides long. (optional)
Protein Coding Sequence [?]
Protein Coding Sequence: enter a nucleotide sequence (at least 50 bp) that encodes a protein, using A/G/C/T/U. Begins with a start codon (ATG/GTG/TTG/CTG). (required)

Target Translation Initiation Rate [?]
Target Translation Initiation Rate: select the desired rate of translation initiation on a proportional scale from 0.1 to 100,000 or more. (required)

Proportional scale (0 to 100,000+) Goal: Maximize
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)

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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.