G4ShapePredictor (G4SP)

G4ShapePredictor is an application designed to accurately predict DNA G4 folding topologies in potassium (K+) buffer based on putative quadruplex sequences. For a detailed examination of the source code used in the paper, please see section on Supplementary Code.

Liew, D., Lim, Z. W., & Yong, E. H. (2024). Machine learning-based prediction of DNA G-quadruplex folding topology with G4ShapePredictor. Scientific Reports, 14(1), 24238.

Installation

G4ShapePredictor.exe (Windows OS only)

If you're using Windows OS, the simplest way to install G4ShapePredictor is to download the .exe file (Google Drive, OneDrive, MediaFire). The files are hosted on an external site due to GitHub's upload limit.

1. Download G4ShapePredictor.zip
2. Unzip G4ShapePredictor.zip
3. Right click G4ShapePredictor.exe > Run as Administrator

If there are errors, include the G4ShapePredictor folder as an exception in Windows Defender, firewall, or any antivirus software you might be using.

Running G4ShapePredictor.py using Python (Windows OS, MacOS, Linux)

WindowsOS

1. Download and install Miniconda
2. Download (or clone) this repository. You may download via: https://github.com/donn-liew/G4ShapePredictor > green "Code" button > download ZIP. Unzip G4ShapePredictor-main.zip.
3. Open Anaconda Prompt from the start menu
4. Run the following command:

conda env create -f path/to/G4ShapePredictor-main/environment.yml

Example: if G4ShapePredictor-main.zip was extracted to my desktop, I would run the following command:

conda env create -f C:/Desktop/G4ShapePredictor-main/environment.yml

5. In Anaconda Prompt, activate the virtual environment by running:

conda activate github-g4predictor

6. Run G4ShapePredictor.py:

python path/to/G4ShapePredictor-main/g4sp application code/G4ShapePredictor.py

MacOS and Linux

1. Download Miniconda
2. Open a terminal window, navigate to the directory containing the downloaded script, and run it with bash Miniconda3-latest-MacOSX-x86_64.sh (adjust the script name as needed for your OS and version). Follow the on-screen prompts.
3. Download (or clone) this repository. You may download via: https://github.com/donn-liew/G4ShapePredictor > green "Code" button > download ZIP.
4. Navigate to the downloaded repository, unzip the file and navigate to the unzipped file:

cd /path/to/downloaded/repository
unzip G4ShapePredictor-main.zip
cd G4ShapePredictor-main

5. Create and activate virtual environment from environment.yml:

conda env create -f environment.yml
conda activate github-g4predictor

6. Run G4ShapePredictor.py:

python g4sp application code/G4ShapePredictor.py