Degenerate Codon Designer

A codon is a sequence of three DNA/RNA nucleotides that corresponds to a specific aminoacid or stop signal during protein synthesis. Naturally, a codon encodes just for one aminoacid. Degenerate nucleotides represent that a certain position can have multiple alternatives from the canonical bases (ATCG). A degenerate codon is a sequence of three degenerate nucleotides which, as a result, encodes for (one or) more than one amino acid.

This program calculates the minimun set of degenerate codons that would encode a given set of amino acids with equal probabilities.

Installation

• Download the repository or clone it into preffered location

git clone https://github.com/beamimc/degenerate_codon_designer.git

Requirements

• python version >= 3.8
• libraries needed:

  pandas==1.3.3
  plotly==4.14.3
  streamlit==1.3.0
  

  • install each by pip install
  • install all by: pip install -r requirements.txt

Description of files

• requirements.txt to install all dependencies
• run_dcg.py is for running program on python enviroment / terminal
• gui.py is for running program on streamlit (https://streamlit.io/)
• create_deg_codons_DB.py is script to generate the datasets/ folder

src/ (module)

• global_variables.py declares global variables of the module
• dcg.py contains degenerateCodon function that calculates the minimum set of degenerate codons given an AAset

datasets/

• contains deg_codons_DB_clean.csv and deg_codons_DB.csv used during the program, created by create_deg_codons_DB.py

static/

images used for the GUI version

• chart.png source is: https://che.gg/3Hhut5V
• logo.svg was made by me

.streamlit/

• config.toml for setting the main theme for the GUI version

How to run

A GUI version of this program was developed, creating a web app using Streamlit (https://streamlit.io/), an open-source Python library. A CLI version was also implemented, so as to run the program on the terminal or python interpreter.

Run GUI version Locally (Recomended)

1. On terminal, move into the folder of the repository downloaded/cloned
2. Type command streamlit run gui.py
3. First time running streamlit a message like this will show. Press enter to skip.

4. A message like the following should show up

5. A new tab in your default browser will automatically open with the app. You can also open it by copying and pasting the Local URL on your browser. Please, note that Safari is not completely compatible. Preferably use Chrome or Firefox.
6. Main page will show, where aminoacids sets can be selected from a list, or from an custom user input (Custom option)

7. Click Design button to run the program and obtain the set of optimized degenerated codons
8. Results will show up, along with some extra information
9. In case any of the provided options were selected (i.e all/KRED/polar/non polar/aromatic), the result will also come with a brief real-work application example

Run CLI version

1. On terminal, move into the folder of the repository downloaded/cloned

2. Type command python run_dcg.py

3. Program will start and ask AAset to the user

4. After input the AAset, program will run and show the results