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.


**  A New and Improved Version of the RBS Calculator Has Been Developed with Greater Predictive Accuracy and a User-Friendly Web Interface  **
The first round of improvements to the RBS Calculator model have been described in:  HM Salis, "The Ribosome Binding Site Calculator", Synthetic Biology: Methods for Building and Programming Life, 19
The second round of improvements to the RBS Calculator model have been described in:  AE Borujeni, AS Channarasappa, HM 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
A new design method, the RBS Library Calculator, for efficient pathway optimization has been described and validated in: I Farasat, M Kushwaha, J Collens, M Easterbrook, M Guido, HM Salis, "Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria", Molecular Systems Biology 10 (6), 2014
A new biophysical model of translational coupling in bacterial operons has been developed and validated in: T Tian, HM Salis, "A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons", Nucleic acids research 43 (14), 7137-7151, 2015 

Additional rounds of model improvements and new design methods for synthetic operons, synthetic riboswitches, synthetic genetic circuits, and optimal metabolic pathways are currently in the process of being published. 


CONTENTS:

File name                           Description
my google colab
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