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.

The Small RNA Calculator

Click here to try an example!


Small RNA Sequence [?]
Small RNA Sequence: enter the nucleotide sequence of a small RNA that binds to mRNA and regulates translation initiation, using A/G/C/T/U. (required).

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)

For Non-Commercial Use Only
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Developed by Amin Espah Borujeni and Howard Salis.
Please inquire about proper citation before using these results in a publication.
Have a Question? Our Documentation, Publications, and References may have your answer!
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.
Method online since January 10th, 2011.