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The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.
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LICENSE
NuPACK.py
RBS_Calculator.py
RBS_MC_Design.py
README
Run_RBS_Calculator.py
Run_RBS_Design.py
ViennaRNA.py

README

This is a software implementation of the Ribosome Binding Site (RBS) Calculator.

The RBS Calculator can predict the translation initiation rate of a protein coding sequence in bacteria. It can also design synthetic ribosome binding site sequences to rationally control the protein expression level. It combines a thermodynamic model of ribosome and mRNA interactions with a sequence optimization algorithm. The RBS Calculator was developed by Howard Salis and Chris Voigt at UC San Francisco.

This software is free software, licensed under the GNU GPL license v3.0.
Copyright is owned by the Regents of the University of California. All rights reserved.
Please read H.M. Salis, E.A. Mirsky, C.A. Voigt, Nature Biotechnology, 2009 for technical details.

CONTENTS:

File name                           Description

RBS_Calculator.py                   Calculates dG_total / translation initiation rate
RBS_MC_Design.py                    Designs synthetic RBS sequences
NuPACK.py                           Python wrapper around NuPACK software package
ViennaRNA.py                        Python wrapper around ViennaRNA software package

Run_RBS_Calculator.py               Command line interface to RBS Calculator
Run_RBS_Design.py                   Command line interface to synthetic RBS designer


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