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

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.
(start typing)

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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.