BGCfinder 0.0.23

Biosynthetic Gene Cluster finder with Graph Neural Network

# 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, [e-mail], [e-mail], https://github.com/jihunni/BGCfinder

To construct the conda environment,

`bash $ conda create --name BGCfinder --clone base $ conda init bash $ conda activate BGCfinder $ conda install pytorch cudatoolkit=11.3 -c pytorch $ conda install pyg -c pyg $ pip install BGCfinder `

To download the BGCfinder model and test files, `bash $ bgc-download `

To run BGCfinder with a fasta file containing amino acid sequence with CPU, `bash bgcfinder bacterial_genome.fasta -o output_filename.tsv -l log_record.log -d False `

To run BGCfinder with a fasta file containing amino acid sequence with GPU, `bash bgcfinder bacterial_genome.fasta -o output_filename.tsv -l log_record.log -d True `

The development environment of BGCfinder : `bash 'torch==1.10.0', 'torch-geometric==2.0.2', 'torch-scatter==2.0.9', 'torch-sparse==0.6.12' `