shenyanxiang / dposfinder

DposFinder

DposFinder is a transformer-based protein language model for phage-encoded depolymerase prediction.

Setup

To install DposFinder, follow these steps：

1. Clone the repository:

git clone https://github.com/shenyanxiang/DposFinder`

2. create a new vertual environment, for example：

cd DposFinder
conda env create -f environment.yml
conda activate DposFinder

3. Download trained DposFinder model from the link below and put it into model directory:

https://tool2-mml.sjtu.edu.cn/DposFinder/model/Final_DposFinder.pt

or you can retrain DposFinder model with optional params by running:

python ./code/main.py [--FLAGS]

params can be checked by command:

python ./code/main.py -h

Usage

Simply use DposFinder to predict depolymerases from protein sequences:

python ./code/main.py --mode predict --data_path ./data --test_data test_set.fasta 

Contact

Please contact Yanxiang shen at [email protected] for questions.