https://github.com/abdelrhman-ellithy/bioinformatics-dna-algorithms
bioinformatics toolkit that integrates various scripts to perform specific tasks in DNA and protein sequence analysis. The project includes a user-friendly GUI developed with Tkinter to manage and execute different bioinformatics algorithms.
https://github.com/abdelrhman-ellithy/bioinformatics-dna-algorithms
Last synced: about 1 month ago
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bioinformatics toolkit that integrates various scripts to perform specific tasks in DNA and protein sequence analysis. The project includes a user-friendly GUI developed with Tkinter to manage and execute different bioinformatics algorithms.
- Host: GitHub
- URL: https://github.com/abdelrhman-ellithy/bioinformatics-dna-algorithms
- Owner: Abdelrhman-Ellithy
- License: mit
- Created: 2024-12-24T19:45:25.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-12-24T19:47:55.000Z (10 months ago)
- Last Synced: 2025-02-16T11:16:11.548Z (8 months ago)
- Language: Python
- Size: 119 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 🐝 Bioinformatics Project
## 📊 Overview
This project is a bioinformatics toolkit that integrates various scripts to perform specific tasks in DNA and protein sequence analysis. The project includes a user-friendly GUI developed with Tkinter to manage and execute different bioinformatics algorithms.
---
## 🎨 Features
- **Interactive GUI**: A Tkinter-based interface to manage and execute bioinformatics scripts.
- **Modular Design**: Individual scripts handle distinct tasks, making the project modular and easy to extend.
- **Automation**: Simplifies the execution of complex bioinformatics algorithms with a click of a button.
---
## 🌐 Prerequisites
- Python 3.x
- Required Libraries:
- `tkinter`
- `subprocess`
- Additional libraries required by individual scripts.
---
## 🔄 Algorithms
### 1. 🔬 Hemolytic Activity Predictor
**Script**: `hemolytic.py`
Predicts the hemolytic activity of peptides based on sequence data. Useful for analyzing peptide stability and toxicity.
---
### 2. 🎲 FASTA File Processor
**Script**: `Fasta_file_processor.py`
Processes FASTA files to extract and manipulate sequence data. Core operations include parsing and validating DNA or protein sequences.
---
### 3. 🍃 DNA Sequence Translator
**Script**: `DNA_sequence_translator.py`
Translates DNA sequences into corresponding RNA or protein sequences. Supports standard genetic code and custom codon tables.
---
### 4. ⚖️ Exact Match Finder
**Script**: `Exact_match_finder.py`
Locates exact matches of query sequences within a larger genome or dataset. Ideal for small-scale pattern searches.
---
### 5. 🔒 Bad Character Heuristic
**Script**: `Bad_character.py`
Implements the bad character rule of the Boyer-Moore string matching algorithm for efficient pattern searching in large datasets.
---
### 6. 🔎 Indexing
**Script**: `Indexing.py`
Constructs data structures like hash tables or k-mer indices to accelerate sequence retrieval and analysis.
---
### 7. 🔐 Suffix Array Construction
**Script**: `Suffix_array.py`
Builds suffix arrays for genome indexing and string matching. A fundamental tool for efficient pattern matching in bioinformatics.
---
### 8. 🌱 Overlap Graph Generator
**Script**: `overlap.py`
Generates overlap graphs from DNA sequences, which are crucial for sequence assembly and alignment tasks.
---
## 📚 How to Use
1. Clone the repository:
```bash
git clone https://github.com/Abdelrhman-Ellithy/bioinformatics-project.git
cd bioinformatics-project
```
2. Ensure all prerequisite libraries are installed.
3. Run the main GUI script:
```bash
python main.py
```
4. Use the buttons in the GUI to execute specific scripts.
---
## 🛠️ Troubleshooting
- Ensure Python is installed and added to your system's PATH.
- Verify the availability of required libraries.
- Check the individual scripts for additional dependencies.
---
## 👨💻 Author
-Abdelrahman Ellithy
---
## 🌐 License
This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for more details.