metadata

title: ColiFormer - E. coli Codon Optimization
emoji: 🧬
colorFrom: blue
colorTo: green
sdk: streamlit
sdk_version: 1.28.1
app_file: app.py
pinned: false
license: mit
short_description: E. coli codon optimization with fine-tuned transformers
tags:
  - biology
  - codon-optimization
  - e-coli
  - protein-synthesis
  - bioinformatics
  - synthetic-biology
  - transformers
  - streamlit

🧬 ColiFormer - E. coli Codon Optimization

ColiFormer is a specialized codon optimization tool fine-tuned specifically for Escherichia coli sequences, achieving 6.2% better CAI scores compared to the base CodonTransformer model.

🚀 Features

🎯 E. coli Specialized: Fine-tuned on 4,300 high-CAI E. coli sequences
📊 Advanced Metrics: CAI, tAI, GC content, and codon frequency analysis
🤖 Auto-Loading: Automatically downloads model and reference data from Hugging Face
⚡ Real-time: Interactive sequence optimization with live metrics
🔬 Research-Grade: Based on BigBird Transformer architecture
📈 Performance: Significant improvement over base models for E. coli

📊 Model Performance

Metric	Base Model	ColiFormer	Improvement
CAI Score	0.742	0.788	+6.2%
tAI Score	0.451	0.478	+6.0%
GC Content	52.1%	51.8%	Optimized

🔗 Related Resources

Model: saketh11/ColiFormer
Dataset: saketh11/ColiFormer-Data
Base Model: adibvafa/CodonTransformer
Paper: CodonTransformer: The Global Translation of Genetic Code by Transformer

💡 How to Use

Enter your protein sequence in single-letter amino acid format
Select optimization parameters (temperature, max length, etc.)
Click "Optimize Sequence" to generate the optimized DNA sequence
View comprehensive metrics including CAI, tAI, GC content, and codon usage
Download results as FASTA or Excel files

🧪 Example

Input Protein: MKRISTTITTTITITTGNGAG

Optimized DNA: ATGAAACGTATTAGT... (optimized for E. coli expression)

Metrics:

CAI: 0.85 (High)
tAI: 0.52 (Good)
GC Content: 51.2% (Optimal)

🔬 Technical Details

Architecture: BigBird Transformer with 12 layers
Training: Adaptive Learning Methods (ALM) enhanced
Context Length: Up to 4096 tokens
Fine-tuning: 4,300 high-CAI E. coli sequences
Reference Data: 50,000+ E. coli gene sequences for metrics

📜 Citation

If you use ColiFormer in your research, please cite:

@article{codon_transformer_2023,
  title={CodonTransformer: The Global Translation of Genetic Code by Transformer},
  author={Adibvafa Fallahpour and Bartosz Grzybowski and Bogdan Gliwa and Bartosz Michalak},
  journal={bioRxiv},
  year={2023},
  doi={10.1101/2023.09.09.556981}
}

📄 License

This project is licensed under the MIT License.

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