VaxLab

VaxLab is an integrated platform for designing optimized mRNA vaccine candidates. This user-friendly tool guides researchers through the complete process of mRNA vaccine design, from antigen input to generating optimized sequences and evaluation.

🎯 Key Features

• Multiple Optimization Strategies: Choose from LinearDesign, CodonBERT, Simple Codon Optimizer, or tissue-specific CUSTOM optimization
• Comprehensive UTR Library: Pre-validated 5' and 3' UTRs from successful commercial vaccines (Pfizer/BioNTech, Moderna)
• Custom UTR Generation: Generate optimized UTRs using GEMORNA or Optimus 5-Prime
• Interactive Visualization: Explore your mRNA construct with an integrated sequence editor and structure viewer
• Quality Assessment: Automated generation of comprehensive optimization reports
• No Coding Required: User-friendly interface accessible to researchers without programming experience

🚀 Quick Start

1. Click the "Open in Colab" badge above
2. Check the "Example Run" box to test with sample data
3. Click Runtime → Run all
4. Observe the optimization process with NanoLuciferase sequence (~1 minute)

📋 Workflow Overview

VaxLab guides you through four simple steps:

1️⃣ Name Your Sequence

Enter a unique identifier for your mRNA construct (e.g., SARS-CoV-2_Spike, mGFP)

2️⃣ Input Your Antigen

• Protein sequences: Single-letter amino acid code (ACDEFGHIKLMNPQRSTVWY)
• DNA/RNA sequences: Nucleotide sequences (automatically translated)

3️⃣ Choose CDS Optimization Strategy

• LinearDesign: Balances mRNA structure and codon optimization
• CodonBERT: AI-based deep learning approach
• Simple Codon Optimizer: Frequency-based codon optimization
• CUSTOM: Tissue-specific optimization (36 human tissues available)

4️⃣ Select UTR Sequences

• 5' UTR: Choose from proven vaccine UTRs or generate custom sequence by using GEMORNA / Optimus 5-Prime
• 3' UTR: Choose from proven vaccine UTRs or generate custom sequence by using GEMORNA
• Option to input your own custom UTR sequences

📊 Output and Analysis

Interactive Results

• Sequence Editor: Color-coded visualization of 5' UTR, CDS, and 3' UTR regions & restriction enzyme cut sites
• Structure Viewer: Interactive RNA secondary structure with folding energy
• Quality Report: Comprehensive analysis with optimization metrics

Key Metrics in Quality Report

• Codon Adaptation Index (CAI): Codon usage optimization score
• GC Content: Sequence composition analysis
• Minimum Free Energy (MFE): RNA structure stability
• DegScore: Predicted mRNA degradation score (Leppek et al., 2022)
• Repeat Analysis: Detection of problematic sequences

Downloadable Files

• FASTA/GenBank: Optimized sequence
• HTML: Quality report
• XLSX: Ready-to-use synthesis order form

⏱️ Performance

• Typical runtime: 1-3 minutes for average proteins (300-500 amino acids)

🎯 Applications

• mRNA Vaccines: SARS-CoV-2, influenza, cancer antigens
• Therapeutic Proteins: Antibodies, enzymes, hormones
• Research Tools: Reporter proteins, research antigens
• Comparative Studies: Multiple optimization strategy evaluation

📚 Citation

If you use VaxLab in your research, please cite:

A pre-print is going to be uploaded soon.

📞 Support

• Issues: Report bugs or request features via GitHub Issues
• Documentation: Full user guide and FAQ available in the notebook
• Contact: Chang Lab, Seoul National University

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

VaxLab integrates several outstanding tools:

• LinearDesign - RNA structure and codon optimization
• CodonBERT - AI-based codon optimization
• Simple Codon Optimizer - Basic frequency-based codon optimization
• CUSTOM - Tissue-specific optimization for targeted expression
• GEMORNA - Deep-learning package for mRNA sequence design
• Optimus-5-Prime - 5' UTR design
• ViennaRNA - RNA structure prediction
• OVE - Teselagen's Open Source Vector Editor

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Developed by Chang Lab, Seoul National University