Simulation of the inhomogeneous TASEP model

Implementation of inhomogeneous TASEP model, the user can input ORF sequences and the elongation rate of each codon to simulate the ribosome dynamics. Supplementary material related to the following paper: https://www.pnas.org/content/116/30/15023.short

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

g++ compiler is needed. The current version has been tested on GCC v4.8.4 and operating system CentOS v7.5.1804

Installing

To compile the program you have to run the following commands:

git clone git@github.com:andreariba/codon_TASEP.git

cd codon_TASEP/simulator

make clean

make

cd ..

Running

Run the simulation for a specific ORF typing the following command

simulator/TASEP_simulator.exe -c <codonspeedfile> -f <elongationspeed> -n <ORFname> -s <ORFsequence>

Arguments:

• -c: tsv file containing an elongation rate for each codon
• -f: double multiplying the codon speeds in the input file in c
• -n: name of the output file
• -s: ORF sequence to simulate

the output includes a file "<ORFname>.dat" containing six columns:

1. factor multiplying the codon speeds (argument -f)
2. initiation rate
3. protein synthesis rate
4. ribosome density
5. fraction of queuing events
6. vector of ribosome density per codon

The file examples.txt includes the list of commands to simulate the model on the yeast translatome

Authors

• Andrea Riba - https://scholar.google.ch/citations?user=aZ9tkZgAAAAJ&hl=en