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
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.
g++ compiler is needed. The current version has been tested on GCC v4.8.4 and operating system CentOS v7.5.1804
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 ..
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:
- factor multiplying the codon speeds (argument -f)
- initiation rate
- protein synthesis rate
- ribosome density
- fraction of queuing events
- vector of ribosome density per codon
The file examples.txt includes the list of commands to simulate the model on the yeast translatome