DNA-Flex

DNA-Flex is a powerful Python library for analyzing DNA sequence flexibility, structure prediction, and advanced genomic analysis using machine learning approaches.

Features

• 🧬 DNA Sequence Analysis

  • Comprehensive sequence analysis
  • Structure prediction
  • Flexibility assessment
  • Mutation impact analysis

• 🤖 AI-Powered Analysis

  • Machine learning models for sequence analysis
  • Deep learning-based structure prediction
  • NLP-based sequence pattern recognition

• ⚡ High-Performance Computing

  • JAX-accelerated computations
  • Async background processing
  • Batch analysis support
  • C++ optimized core components

• 🔄 API Integration

  • RESTful API with FastAPI
  • JWT Authentication
  • Rate limiting
  • Background task processing
  • Swagger/OpenAPI documentation

Quick Start

Installation

# Basic installation
pip install dnaflex

# Development installation
git clone https://github.com/vishwamai/DNA-Flex.git
cd DNA-Flex
pip install -e '.[dev]'

Basic Usage

from dnaflex.models.analysis import analyze
from dnaflex.models.dynamics import molecular_dynamics

# Analyze DNA sequence
sequence = "ATGCTAGCTAGCT"
result = analyze(sequence)
print(f"GC Content: {result['gc_content']}%")
print(f"Flexibility Score: {result['flexibility_score']}")

# Run molecular dynamics simulation
dynamics = molecular_dynamics.simulate(sequence)

API Usage

import requests

# Get authentication token
response = requests.post(
    "http://localhost:8000/token",
    data={"username": "your-username", "password": "your-password"}
)
token = response.json()["access_token"]

# Analyze sequence
headers = {"Authorization": f"Bearer {token}"}
response = requests.post(
    "http://localhost:8000/predict",
    headers=headers,
    json={"sequence": "ATGCTAGCTAGCT"}
)
result = response.json()

Architecture

DNA-Flex is built with a modular architecture:

• Core Analysis Engine: Built in Python with C++ extensions
• Machine Learning Models: Using JAX and deep learning
• REST API: FastAPI with async processing
• Data Management: Efficient caching and data providers

API Documentation

Visit our API Documentation for detailed endpoint information.

Development Guide

See our Developer Guide for setup and contribution guidelines.

Project Structure

dnaflex/
├── models/          # Core analysis models
├── structure/       # Structure handling
├── flexibility/     # Flexibility analysis
├── parsers/         # File format parsers
├── data/           # Data management
└── tests/          # Test suite

Configuration

Environment variables:

• DNA_FLEX_SECRET_KEY: JWT secret key
• DNA_FLEX_API_PREFIX: API prefix (default: /api/v1)
• DNA_FLEX_RATE_LIMIT: Rate limit (requests/minute)

Testing

# Run all tests
pytest

# Run specific test suite
pytest dnaflex/tests/test_integration.py

Contributing

Please read our Contributing Guidelines before submitting pull requests.

License

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

Citation

If you use DNA-Flex in your research, please cite:

@software{dna_flex_2025,
  title = {DNA-Flex: DNA Sequence Analysis and Structure Prediction},
  author = {kasinadhsarma},
  year = {2025},
  url = {https://github.com/yourusername/DNA-Flex}
}