Deep learning prediction of influenza virus pathogenicity from HA cleavage sites
Project description
FluCleave
Deep learning prediction of influenza virus pathogenicity from HA cleavage sites.
Features
- Analyzes hemagglutinin (HA) cleavage site sequences
- Predicts high/low pathogenicity using deep learning
- Handles both DNA and protein sequences
- Command-line interface for easy use
- Trained on curated dataset of known pathogenic sequences
Installation
pip install flucleave
Usage
Predict pathogenicity from FASTA file:
flucleave predict --fasta sequences.fasta --output-dir results/
Train new model (optional):
flucleave train --training-csv data.csv
Data Format
Input FASTA should contain HA protein sequences. Example:
>A/chicken/Hong_Kong/220/97
MVNQILIILAAIASAAPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDI...
Or DNA sequences. Example:
>A/chicken/Hong_Kong/220/97
ATGGAAGGCAATACTAGTAGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT...
License
FluCleave is licensed under the MIT License.
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