Codes for "Computational design and interpretation of single-RNA translation experiments"

Luis U. Aguilera, William Raymond, Zachary Fox, Michael May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, and Brian Munsky.

Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO, 80523, USA
Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, 80523, USA
World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan

For questions about the codes, please contact: Luis.aguilera@colostate.edu and brian.munsky@colostate.edu

---

This repository contains the codes necessary to reproduce figures from the above manuscript. All codes are implemented in Matlab 2018.

Code organization

The codes are organized on the following categories.

• Computes the sequence properties.
  

  masterFunction_Kymograph.m
  masterFunction_RibosomeOccupancy.m
  masterFunction_Collisions_RibosomeDensity.m
  

• Computes the parameter estimation routines and parameter uncertainty.

  masterFunction_ParameterEstimation.m
  masterFunction_ParameterUncertainty.m
  

• Computes the elongation methods (FRAP, FCS, and ROA) for the example genes (H2b, beta-actin, KDM5B).
  

Mean values

masterFunction_Mean_AC.m
masterFunction_Mean_FRAP.m
masterFunction_Mean_ROA.m

Mean values with standard deviation

masterFunction_SD_AC.m
masterFunction_SD_FRAP.m
masterFunction_SD_ROA.m

• Computes the elongation methods for a library of human genes. (FRAP, FCS, and ROA).
  

masterFunction_TableOfGenes.m
masterFunction_GeneLibrary_REP_AC.m
masterFunction_GeneLibrary_REP_FRAP.m
masterFunction_GeneLibrary_REP_ROA.m

• Computes the codon optimization experiments.
  

masterFunction_CodonOptimization.m

• Computes the tRNA depletion experiments.
  

masterFunction_tRNA_Depletion.m

---

Experimental data.

• Autocorrelation data
  actBIntensityData.xls
  h2bIntensityData.xls
  kdmIntensityData.xls
  

• Intensities data
  intensities_Bact.xlsx
  intensities_H2B.xlsx
  intensities_KDM5B.xlsx
  

---

Gene Sequences.

H2B_withTags.txt
Bactin_withTags.txt
KDM5B_withTags.txt

The list of human genes used in this study is given in:

DB_Genes.xlsx

---

Code implementation.

The codes performing the optimization and uncertainty (masterFunction_ParameterEstimation.m and masterFunction_ParameterUncertainty.m), rely upon expensive computations that were performed on the W.M. Keck Compute Cluster.

Additional notes

The codes are compiled to run in Mac OS and Linux OS. If there is a conflict with the user operative system. Try the following steps: 1) Open Matlab. 2) Open the directory. 3) double click on the file SSA_longNames.prj 4) Generate a MEX-file with Matlab Coder.