DNA-Sequence-Analyzer

A robust Python-based bioinformatics tool for comprehensive DNA sequence analysis and manipulation.

Features

• GC Content Analysis: Precise calculation of GC content percentage
• Nucleotide Frequency: Detailed nucleotide distribution analysis
• Motif Finding: Advanced pattern recognition and position reporting
• Sequence Manipulation: Generate complement and reverse complement sequences
• Gene Detection: Identification of potential coding regions using start/stop codons
• FASTA Support: Full support for standard FASTA file format

Installation

1. Clone the repository:

git clone https://github.com/yourusername/dna_analyzer.git
cd dna_analyzer

2. Install dependencies:

pip install -r requirements.txt

Usage

Basic Analysis

python src/main.py -i data/example1.fasta -o results.txt -a

Motif Search

python src/main.py -i data/example2.fasta -m ATCG -o motif_results.txt

Command Line Arguments

• -i, --input: Input FASTA file path
• -o, --output: Output file path for results
• -a, --analyze: Perform complete sequence analysis
• -m, --find-motif: Search for specific DNA motif

Example Data

The repository includes two example FASTA files in the 'data/' directory:

• example1.fasta: Contains human and mouse gene sequences
• example2.fasta: Contains COVID-19 spike protein and insulin gene fragments

Testing

Run the test suite:

pytest tests/

Project Structure

dna_analyzer/
├── src/
│   ├── sequence_analyzer.py
│   ├── utils.py
│   └── main.py
├── tests/
│   └── test_analyzer.py
├── data/
│   ├── example1.fasta
│   └── example2.fasta
└── docs/

Technical Details

• Python 3.8+
• Modular architecture for easy extension
• Comprehensive test coverage
• Efficient sequence processing algorithms

Contributing

• Fork the repository
• Create your feature branch (git checkout -b feature/AmazingFeature)
• Commit your changes (git commit -m 'Add some AmazingFeature')
• Push to the branch (git push origin feature/AmazingFeature)
• Open a Pull Request

License

Distributed under the MIT License. See LICENSE for more information.