EPC-codon-optimizer

Codon optimizer for Escherichia, Pseudomonas and Caulobacter.

Table of Contents

• Overview
• Installation
• Usage
• Contributing
• License

Overview

The EPC codon optimizer is a Python tool designed for creating nucleotide sequences optimized for expression in Escherichia coli MG1655, Pseudomonas aeruginosa PAO1 and Caulobacter vibrioides NA1000. It can serve as a first step in codon optimization for gene synthesis. The tool can be run locally either via the command line or through a graphical user interface (GUI) built with Streamlit. Alternatively, the GUI can be accessed directly online via Streamlit Cloud.

For more details about the project, refer to the accompanying PDF file 'Rationale for EPC codon optimization'.

Installation

⚠️ Note: The following instructions are for local use only.
If you prefer to use the app online via Streamlit Community Cloud, there is nothing to install, simply visit:
👉 Launch the app on Streamlit Cloud

1. Clone the repository:

   git clone https://github.com/annefrancezcharlot/EPC-codon-optimizer.git
   cd EPC-codon-optimizer

   or

   Go to https://github.com/annefrancezcharlot/EPC-codon-optimizer and download the zip file and unzip it

2. Create a virtual environment:

   python -m venv environment_name

3. Activate the virtual environment:

   • On Windows:

     environment_name\Scripts\activate

   • On macOS/Linux:

     source environment_name/bin/activate

4. Install the required dependencies:

   • For CLI use

     pip install -r requirements.txt

   • FOR GUI use locally

     pip install -r requirements-streamlit.txt

Usage

Note: The input file must contain protein sequences in standard FASTA format.

• To use the app on Streamlit Community Cloud, visit:

  https://epc-codon-optimizer-main.streamlit.app/

• For CLI usage:

  python epc_opt.py input_sequences.fasta output_sequences.txt

  • input_sequences.fasta: Path to your input FASTA or text file containing protein sequences.
  • output_sequences.txt: Path to the output file where optimized nucleotide sequences will be written.

• FOR GUI usage locally:

  streamlit run optimize_app.py

Contributing

We welcome contributions to the EPC codon optimizer!

License

This project is licensed under the MIT License.