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https://github.com/code-jl/dna-sequence-analyzer
https://github.com/code-jl/dna-sequence-analyzer
Last synced: 3 days ago
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- Host: GitHub
- URL: https://github.com/code-jl/dna-sequence-analyzer
- Owner: Code-JL
- License: mit
- Created: 2025-01-05T23:43:04.000Z (15 days ago)
- Default Branch: main
- Last Pushed: 2025-01-06T00:15:41.000Z (15 days ago)
- Last Synced: 2025-01-06T01:22:59.003Z (15 days ago)
- Language: Scala
- Size: 8.79 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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:
```bash
git clone https://github.com/yourusername/dna_analyzer.git
cd dna_analyzer
```
2. Install dependencies:
```bash
pip install -r requirements.txt
```
## Usage
## Basic Analysis
```bash
python src/main.py -i data/example1.fasta -o results.txt -a
```
## Motif Search
```bash
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:
```bash
pytest tests/
```
## Project Structure
```bash
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](LICENSE) for more information.