Biosynthetic Gene Cluster finder with Graph Neural Network
Project description
# BGCfinder : Biosynthetic Gene Cluster detection with Graph Neural Network
BGCfinder detects biosynthetic gene clusters in bacterial genomes using deep learning. BGCfinder takes a fasta file containing bacterial protein coding sequences and embed each protein sequence into a graph. Graph Neural Network takes the graphs to detect biosynthetic gene cluster.
Author : Jihun Jeung, jihun@gm.gist.ac.kr, jeung4705@gmail.com, https://github.com/jihunni/BGCfinder
To run BGCfinder with a fasta file containing amino acid sequence with CPU, `bash python BGCfinder/main.py data/test_run.fasta -o test_run.tsv -l test_run.log -d False `
To run BGCfinder with a fasta file containing amino acid sequence with GPU, `bash python BGCfinder/main.py data/test_run.fasta -o test_run.tsv -l test_run.log -d True `
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