DeepBGC - Biosynthetic Gene Cluster detection and classification
DeepBGC: Biosynthetic Gene Cluster detection and classification
DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. DeepBGC employs a Bidirectional Long Short-Term Memory Recurrent Neural Network and a word2vec-like vector embedding of Pfam protein domains. Product class and activity of detected BGCs is predicted using a Random Forest classifier.
Install using bioconda (recommended)
- Install Bioconda by following Step 1 and 2 from: https://bioconda.github.io/
conda install deepbgcto install DeepBGC and all of its dependencies
Install using pip
If you don't mind installing the HMMER and Prodigal dependencies manually, you can also install DeepBGC using pip:
- Install Python version 2.7+ or 3.4+
- Install Prodigal and put the
prodigalbinary it on your PATH: https://github.com/hyattpd/Prodigal/releases
- Install HMMER and put the
hmmpressbinaries on your PATH: http://hmmer.org/download.html
pip install deepbgcto install DeepBGC
Download models and Pfam database
Before you can use DeepBGC, download trained models and Pfam database:
You can display downloaded dependencies and models using:
Detection and classification
Detect and classify BGCs in a genomic sequence. Proteins and Pfam domains are detected automatically if not already annotated (HMMER and Prodigal needed)
# Show command help docs deepbgc pipeline --help # Detect and classify BGCs in mySequence.fa using DeepBGC algorithm and save the output to mySequence directory. deepbgc pipeline mySequence.fa
This will produce a directory with multiple files and a README.txt with file descriptions.
You can train your own BGC detection and classification models, see
deepbgc train --help for documentation and examples.
DeepBGC positives, negatives and other training and validation data can be found on the releases page.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|deepbgc-0.1.6-py3-none-any.whl (58.5 kB) Copy SHA256 hash SHA256||Wheel||py3|
|deepbgc-0.1.6.tar.gz (41.5 kB) Copy SHA256 hash SHA256||Source||None|