dsites 1.1.0

D-Sites: Hybrid TFBS predictor (PWM + DNA shape + RF)

D-Sites: Hybrid TFBS Predictor for Bacterial Genomes

A comprehensive computational tool for predicting transcription factor binding sites (TFBS) in bacterial genomes using hybrid PWM, DNA shape features, and Random Forest classification.

🚀 Quick Start

Installation

## Quick Start
git clone https://github.com/yourusername/dsites.git
cd dsites
pip install -r requirements.txt

Basic Prediction

python src/D-Sites.py --fasta examples/AmrZ/genome.fasta \
                     --gff examples/AmrZ/annotation.gff \
                     --motif examples/AmrZ/motif.meme \
                     --gene AmrZ \
                     --genome_accession NC_002516.2

Run Benchmarking

# Comprehensive benchmarking
python scripts/fullbench.py

# FNR-specific analysis
python scripts/fimo_fnr.py

# Generate validation plots
python scripts/generate_pr_curves.py

📊 Available Scripts

• src/D-Sites.py: Main prediction pipeline
• scripts/fullbench.py: Comprehensive performance evaluation
• scripts/comprehensive_validation.py: Validation across all TFs
• scripts/fimo_fnr.py: FNR-specific FIMO comparison
• scripts/generate_pr_curves.py: Precision-Recall curve generation
• scripts/generate_enrichment_plot.py: Promoter enrichment analysis
• scripts/master_analysis.py: Master analysis script

🧪 Validation Datasets

Complete validation data for four transcription factors:

• AmrZ: Pseudomonas aeruginosa PAO1
• GlxR: Corynebacterium glutamicum R
• CodY: Bacillus anthracis Sterne
• FNR: Salmonella enterica Typhimurium

📈 Performance

D-Sites demonstrates:

• Up to 9.3× higher recall than FIMO
• 3-4× higher precision in top predictions
• 3.02-3.42× enrichment in promoter regions
• 68.1% validation success for FNR regulon

📝 Citation

If you use D-Sites in your research, please cite:

Pankaj et al. (2025). D-Sites: A computationally efficient tool for predicting protein binding sites in bacterial genomes. Journal Name, Volume, Pages.

📄 License

MIT License - see LICENSE for details.

💬 Contact

For questions and support, please open an issue on GitHub or contact [e-mail].