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NPBDetect: A Neural network model to detect bioactivities from Antismash GBK files

NPBDetect is available in:

Contents

CLI installation

  1. Setup conda environment

conda create -n npbdetect python=3.10

  1. Install packages with pip
conda activate npbdetect
pip3 install pandas
pip3 install scikit-learn
pip3 install biopython
pip3 install torch torchaudio torchvision torchtext torchdata
  1. Clone repository

git clone git@

  1. Test samples to validate installation

python NPBDetect.py predict --gbk test/BGC0000004.gbk --pred HC --out_dir outs/

Google Colab

Click on link to use google colab without setting up locally:

NPBDetect@google-colab

Jupyter Notebook

Use local jupyter notebook as

Docker

For docker users

Usage

  1. Generate GBK files with antiSMASH 7 Use following command to generate GBK file:

    antismash

  2. Use any version of NPBDetect to predict bioactivity

If you use the code, please cite the paper:

Hemant Goyat, Dalwinder Singh Sunaina Paliyal, Mohit Panghal, Shrikant Mantri , Predicting biological activity from biosynthetic gene clusters using neural networks), 2024.