🧬 GeneAligner

Interactive Sequence Alignment Tool for DNA & RNA

Created by Bano Rani — for educational purposes

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📖 Overview

GeneAligner is a beginner-friendly bioinformatics web app built with Streamlit that helps users perform and visualize DNA/RNA sequence alignments using multiple classic alignment techniques:

Method	Type	Description
🔹 Dot Matrix	Visual	Graphical comparison of sequence similarity
🔹 Needleman-Wunsch	Global Alignment	Aligns sequences end-to-end
🔹 Smith-Waterman	Local Alignment	Finds best matching subsequences
🔹 Word Method	Heuristic	Fast approximate alignment via k-mer matching

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📸 Preview

  

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🚀 Features

• ✅ Upload or type DNA/RNA sequences
• ✅ Clean and validate sequences automatically
• ✅ Choose from multiple alignment algorithms
• ✅ Visualize alignment steps and scoring matrices
• ✅ Download or copy alignment results

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🧠 Use Cases

• 🧬 Teaching bioinformatics alignment concepts
• 🧪 Practicing global vs. local alignment
• 👩‍🏫 Classroom demos for biology students
• 💻 Hands-on project for beginners in bioinformatics

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Visual Result

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🛠️ Installation

1. Clone the repository

git clone https://github.com/Bano733-code/gene-aligner-app.git
cd gene-aligner-app

2. Create a virtual environment (recommended)

python -m venv venv
source venv/bin/activate      # On Windows: venv\Scripts\activate

3. Install dependencies

pip install -r requirements.txt

4. Run the app

streamlit run app.py

The app will open automatically in your browser at http://localhost:8501.

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▶️ Usage

1. Launch the app using the command above.
2. Enter or upload your DNA/RNA sequences in the input panel.
3. Select an alignment method — Dot Matrix, Needleman-Wunsch, Smith-Waterman, or Word Method.
4. Click Align to view the result and scoring matrix.
5. Download or copy the alignment output for your report or assignment.

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📁 Project Structure

gene-aligner-app/
├── figures/                  # Images used in README and app
├── app.py                   # Main Streamlit application
├── alignment/                # Alignment algorithm modules
│   ├── dot_matrix.py
│   ├── needleman_wunsch.py
│   ├── smith_waterman.py
│   └── word_method.py
├── requirements.txt
├── LICENSE
└── README.md

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🧩 Tech Stack

• Python 3.9+
• Streamlit — web interface
• NumPy — matrix computations
• Matplotlib / Plotly — alignment visualization

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🤝 Contributing

Contributions are welcome! To contribute:

1. Fork the repository
2. Create a new branch (git checkout -b feature/your-feature)
3. Commit your changes (git commit -m "Add your feature")
4. Push to the branch (git push origin feature/your-feature)
5. Open a Pull Request

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📜 License

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

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💡 Credits

• Created with ❤️ using Streamlit
• Bioinformatics algorithms adapted for educational use
• Developed by Bano Rani

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_{⭐ If you found this project helpful, consider giving it a star on GitHub!}