Our new paper is out: Farasat et. al. "Efficient search, mapping, and optimization of multiā€protein genetic systems in diverse bacteria", Molecular Systems Biology, v10(6), 2014.

Some highlights: The RBS Library Calculator is extensively validated on 600+ genetic systems encoded on plasmids and within genomes. Our biophysical model's predictions are accurate in the industrially relevant hosts E. coli BL21, Bacillus subtilis, Pseudomonas putida, and Corynebacterium glutanicum, demonstrating that ribosome-RNA physical interactions remain the same across different organisms. Sequence optimization and system-wide kinetic modeling allows you to predict, control, and maximize the productivity of a multi-enzyme metabolic pathway. Flux control coefficients quantify the rate-limiting steps in a pathway, its optimality, and indicate when alternative genes and pathways should be targeted to further increase biosynthesis rates.

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.
(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: 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.
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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.