Welcome to rbsXpress!
rbsXpress is a platform for the prediction and forward engineering of
ribosome binding site (RBS)
strength to control protein levels in procaryotes.
It is composed of the following two tools:
RBS Predictor
The
RBS Predictor is the core model of rbsXpress and is based on a deep-learning model (
SAPIENs) that was trained on approximately 250,000 experimentally characterized RBS sequences.
It accepts
5’-UTR sequences as an input and predicts their relative translation rate (
rTR) as main output.
Furthermore, it can be used to generate input data for the RBS library tool
RedLibs (see below). More details on the prediction model and the underlying data generation can be found in the following publication:
- Höllerer, S., Papaxanthos, L., Gumpinger, A. C., Fischer, K., Beisel, C., Borgwardt, K., Benenson, Y., & Jeschek, M. (2020).
Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.
Nature communications, 11(1), 3551
(https://doi.org/10.1038/s41467-020-17222-4)
RedLibs
RedLibs is a tool for the generation of RBS libraries. It uses RBS prediction data as input and computes
degenerate sequences
that encode several RBSs which uniformly span the accessible rTR range (i.e. from low to high RBS strength).
The user defines the number of individual RBSs encoded by the degenerate sequence (i.e. the library size).
The resulting “smart” RBS libraries can be simply cloned in bulk and subsequently used to systematically
search for optimal expression levels, either for individual proteins or within multi-protein systems. More
details on
RedLibs as well as a use case in metabolic pathway optimization are described in the following
publication:
- Jeschek, M., Gerngross, D., & Panke, S. (2016).
Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.
Nature communications, 7, 11163
(https://doi.org/10.1038/ncomms11163)
Tips and tricks
- For inexperienced users, it is highly recommended to consult the Glossary and different mouseovers to familiarize yourself with RBS engineering and the provided tools.
- Why register? While all tools of rbsXpress can be accessed without an account, we recommend to sign up. It will only take one minute and allow you to conveniently store and access previous results.
Legal Disclaimer
This website is free to all users and licensed under CC BY-ND 4.0.
All tools provided on this website are for synthetic biology research and educational purposes. While efforts have been made to ensure the accuracy and reliability of the tools, they are provided "as is" without warranty of any kind, express or implied, including but not limited to warranties of merchantability, fitness for a particular purpose, or non-infringement.
By using this tool, you acknowledge and agree that: The tools’ outputs are generated based on computational models and algorithms that may have limitations or inaccuracies. The developers, contributors, and distributors of this tool shall not be held liable for any direct, indirect, incidental, consequential, or punitive damages, including but not limited to loss of data, profits, or research opportunities, arising out of or related to your use or inability to use the tool. It is your responsibility to ensure that all use of the tool and any subsequent research or application complies with applicable laws, regulations, and ethical standards. The developers of this tool are not responsible for any misuse or unlawful activity arising from its use.
Data you provide may be collected and stored solely for the purpose of delivering and improving the service, which includes generating statistical insights to enhance user experience. We are committed to safeguarding your data and will not share, sell, or otherwise distribute your information to third parties, except as required by law.