These scripts and datasets were created for the codon evolution rotation project in the Wilke lab, Winter 2018-2019
Broad scope: in-silico directed evolution experiment that utilizes pinetree to simulate transcription and translation rates.
Rationale: presence of codon ramps at the 5’ and 3’ end of mRNAs could be a biological mechanism for controlling speed of protein production in highly translated genes (Tuller and Zur 2014). In addition, ramps are observed in Ashley’s programthat may be of biological significance, or an artifact of the program (TASEP ribosomal model used in her translational modeling tool). To read more, visit https://sites.google.com/utexas.edu/codonramps/home
Requirements
- Python 3.7.0
- NumPy v1.15
- Pandas
- Pinetree https://github.com/benjaminjack/pinetree
Usage To begin simulation of a transcript with a slow rate of 0.5 (-s option) and a fast rate of 1.0 (-f option) for one generation (-g option), navigate to script directory and enter:
python3 pooled_evolution.py -g 1 -s 0.5 -f 1.0 -o output_directory