BioSequence Analyzer API

A powerful FastAPI-based Bioinformatics API for DNA sequence analysis. The project provides nucleotide composition analysis, GC/AT content calculation, DNA-to-RNA transcription, protein translation, mutation detection, ORF detection, restriction enzyme analysis, primer design, sequence alignment, phylogenetic analysis, and automated report generation.

The API supports both single-sequence analysis and batch processing through FASTA file uploads, making it useful for bioinformatics research, education, and software development.

Features

• DNA sequence validation
• Nucleotide composition analysis
• GC & AT content calculation
• DNA → RNA transcription
• Protein translation
• Reverse complement generation
• Mutation detection
• Mutation summary
• ORF (Open Reading Frame) detection
• Restriction enzyme site analysis
• Molecular weight calculation
• Melting temperature (Tm)
• Needleman–Wunsch sequence alignment
• Primer design
• FASTA file upload & batch analysis
• Multiple sequence comparison
• Phylogenetic distance matrix
• Newick tree generation
• JSON report generation
• PDF report generation
• Interactive Swagger API documentation

Project Structure

BioSequence-Analyzer-API/
│
├── constants/
│   ├── __init__.py
│   ├── codon_table.py
│   └── dna.py
│
├── features/
│   ├── alignment.py
│   ├── enzymes.py
│   ├── multiple_alignment.py
│   ├── orf.py
│   ├── phylogeny.py
│   ├── primer.py
│   └── properties.py
│
├── reports/
│   ├── report_generator.py
│   └── pdf_report.py
│
├── sample_data/
│   └── sample.fasta
│
├── analyzer.py
├── main.py
├── models.py
├── parser.py
├── requirements.txt
├── README.md
└── LICENSE

Technologies Used

• Python 3.11+
• FastAPI
• Pydantic
• Uvicorn
• Biopython
• ReportLab
• NumPy
• Matplotlib (for future visualization)

Installation

Clone the repository:

git clone https://github.com/YOUR_USERNAME/BioSequence-Analyzer-API.git

Move into the project directory:

cd BioSequence-Analyzer-API

Install dependencies:

pip install -r requirements.txt

Running the API

Start the FastAPI server using Uvicorn:

uvicorn main:app --reload

The API will start at:

http://127.0.0.1:8000

---

API Documentation

FastAPI automatically generates interactive API documentation.

Swagger UI

http://127.0.0.1:8000/docs

ReDoc

http://127.0.0.1:8000/redoc

API Endpoints

Method	Endpoint	Description
GET	/	API welcome message
POST	/analyze	Analyze a DNA sequence
POST	/upload-fasta	Upload and analyze FASTA file
POST	/generate-report	Generate analysis report

Example Request

{
  "sequence": "ATGCGTGAATTCGCGTAA",
  "reference": "ATGCGTGAATTCGCGTAA"
}

Example Response

{
  "sequence_analysis": {
    "sequence": "ATGCGTGAATTCGCGTAA",
    "length": 18,
    "reverse_complement": "TTACGCGAATTCACGCAT"
  },
  "composition": {
    "GC_content": 50.0,
    "AT_content": 50.0
  },
  "translation": {
    "protein": "MREFA"
  }
}

Screenshots

Swagger UI

Add a screenshot of the interactive Swagger documentation.

---

Example Analysis

Add a screenshot showing a successful DNA sequence analysis.

---

FASTA Upload

Add a screenshot of batch sequence analysis.

Future Roadmap

• 📊 DNA sequence visualization
• 📈 GC content and nucleotide composition charts
• 🗄️ Database integration (SQLite / PostgreSQL / MongoDB)
• 👤 User authentication
• 📜 Analysis history
• 🤖 Machine Learning-based mutation prediction
• 🧬 Disease classification models
• 🐳 Docker support
• ☁️ Cloud deployment
• 🌐 Public API endpoint

Contributing

Contributions are welcome!

If you'd like to improve this project:

1. Fork the repository.
2. Create a new feature branch.
3. Commit your changes.
4. Open a Pull Request.

License

This project is licensed under the MIT License.

Author

Muhammad Moeen Asim

Bioinformatics Student | Python Developer | FastAPI Developer

• GitHub: https://github.com/MoeenAsim
• LinkedIn: https://www.linkedin.com/in/muhammad-moeen-asim-679209332/