sequence-alignment-app

This project implements a sequence alignment application with a Python backend and a React frontend. The backend generates two identical DNA sequences with random mutations and implements the Needleman-Wunsch algorithm for sequence alignment. The frontend visualizes the sequences and allows users to control the mutation rate through a slider.

Project Structure

sequence-alignment-app
├── backend
│   ├── app.py                # Entry point for the Flask backend
│   ├── needleman_wunsch.py   # Implementation of the Needleman-Wunsch algorithm
│   ├── sequence_generator.py  # Functions to generate random DNA sequences
│   ├── requirements.txt       # Python dependencies for the backend
│   └── README.md              # Documentation for the backend
├── frontend
│   ├── public
│   │   └── index.html         # Main HTML file for the React application
│   ├── src
│   │   ├── App.js             # Main component of the React application
│   │   ├── components
│   │   │   ├── SequenceVisualizer.js  # Component to visualize sequences
│   │   │   └── MutationRateSlider.js  # Component for controlling mutation rate
│   │   └── index.js           # Entry point for the React application
│   ├── package.json           # Configuration file for npm
│   └── README.md              # Documentation for the frontend
└── README.md                  # Overview of the entire project

Backend Setup

1. Navigate to the backend directory.
2. Install the required dependencies:

   pip install -r requirements.txt
   

3. Run the Flask application:

   python app.py
   

Frontend Setup

1. Navigate to the frontend directory.
2. Install the required dependencies:

   npm install
   

3. Start the React application:

   npm start
   

Usage

• The backend API will generate two sequences with a specified mutation rate.
• The frontend allows users to visualize the sequences and adjust the mutation rate using a slider.
• The aligned portions of the sequences will be highlighted in the visualization.