The Salis Lab has recently discovered a new mechanism, called Ribosome Drafting, that controls a mRNA's translation rate. Learn more about it in our latest publication: Espah Borujeni and Salis. Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism, Journal of the American Chemical Society, 2016

Are you engineering riboswitches? See our latest NAR Breakthrough Article Automated physics-based design of riboswitches from diverse RNA aptamers, Nucleic Acid Research, 2016. Are you engineering bacterial operons? In non-model hosts? Then our latest published work should also interest you: Kushwaha and Salis, A Portable Expression Resource for Engineering Cross-species Genetic Circuits and Pathways, Nature Communications, 2015. and Tian and Salis, A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons, Nucleic Acid Research, 2015

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)

RBS Constraints [?]
Ribosome Binding Site Sequence Constraints: enter a degenerate nucleotide sequence that determines which mutations to the RBS are allowable. Insert a N where mutations are desired or A/G/C/T/U where mutations are not desired. (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
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: 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.

Version 2.0: Includes additional interactions between the ribosomal platform and mRNA at upstream standby sites. These changes are described in Espah Borujeni, Channarasappa, and Salis, Nucleic Acid Research, v42 (4), 2014.

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.
(start typing)

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For Non-Commercial Use Only. Click here for commercial usage.
Have a Question? Our Documentation, Publications, and References may have your answer!
When using these results, please reference A. Espah Borujeni, A.S. Channarasappa, and H.M. Salis, "Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites", Nucleic Acid Research, 2013 and H.M. Salis, E.A. Mirsky, C.A. Voigt, Nat. Biotech., 2009
We gratefully acknowledge research funding from the Air Force Office of Scientific Research, 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.