🧬 GeneStudio

A Modern GUI Toolkit for DNA Sequence Analysis & Bioinformatics Algorithms

GeneStudio is a desktop application built in Python that brings powerful DNA sequence analysis tools and classical string-matching algorithms into a clean, intuitive GUI.

It is designed for students, researchers, and developers who need to explore DNA sequences using both basic biological operations and advanced computational algorithms — without requiring deep bioinformatics knowledge.

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🚀 Features

🔹 Sequence Processing

• Load and parse FASTA files
• GC% calculation
• Reverse, Complement, Reverse-Complement
• DNA → Amino Acid Translation using a codon table
• Scrollable sequence viewer with colored highlighting

🔹 Exact Pattern Matching

• Boyer–Moore (Bad Character Rule)
• Boyer–Moore (Good Suffix Rule)
• Suffix Array construction
• Inverse Suffix Array
• Exact search via suffix array
• Visual highlighting of match positions

🔹 Approximate Matching

• Hamming Distance search
• Edit Distance (Dynamic Programming)
• Threshold-based approximate matching

🔹 Graph Algorithms

• Overlap Graph construction from multiple FASTA sequences
• Adjustable minimum overlap length
• Adjacency list view + optional graphical visualization

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🖥️ GUI Overview (Screenshots)

(Add your screenshots here later)

📂 File           🔍 Pattern Matching
🧬 Sequence       🎯 Approximate Matching
🧪 Operations     🕸️ Overlap Graph

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🧩 Algorithms Implemented

Category	Algorithms
Sequence Ops	GC%, Reverse, Complement, Reverse-Complement
Translation	DNA → Amino Acids
Exact Matching	Boyer–Moore (Bad Char), Boyer–Moore (Good Suffix), Suffix Array, Inverse SA
Approx Matching	Hamming Distance, Edit Distance (DP)
Graphs	Overlap Graph

All algorithms are implemented from scratch — no external bioinformatics libraries.

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🏗️ Project Structure

GeneStudio/
│
├── gui/                     # GUI components
├── algorithms/              # Core algorithms
├── assets/                  # Icons & images
├── main.py                  # Application entry point
└── README.md

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📦 Installation

1. Clone the repository:

git clone https://github.com/<your-username>/GeneStudio.git
cd GeneStudio

2. Install dependencies:

pip install -r requirements.txt

3. Run the app:

python main.py

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⚙️ Technologies Used

• Python 3.10+
• PyQt5 / PySide6 (GUI)
• NetworkX (optional graph visualization)
• Standard Python algorithms (no heavy external libraries)

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📘 Documentation

A full Software Requirements Specification (SRS) is included, covering:

• System statement
• Functional requirements
• Non-functional requirements
• Formal algorithmic properties

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🎯 Purpose of the Project

GeneStudio is an educational yet powerful tool that demonstrates how classical data-structure and string-matching algorithms can be applied to real biological sequences.

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🤝 Contributing

Contributions, issues, and feature requests are welcome!

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📄 License

This project is licensed under the MIT License.

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