Protein Swirl is a website to search, analyse, and visualise protein sequences by taxon and family. Built for the Introduction to Website and Database Design (BILG11016) course at the University of Edinburgh, it combines sequence retrieval, multiple sequence alignment, motif detection, and visualisation — all wrapped in a simple user interface.
- To combine web development with a bioinformatics workflow.
- To deepen understanding of backend scripting (Bash/Python) and database driven applications.
- To explore the integration of biological analysis tools (Clustal Omega, EMBOSS) into a web context.
Clone the repository and set up a local web server (e.g. XAMPP, LAMP):
git clone https://github.com/cemileblks/bioinf-web-project- Import the provided
.sqlfile into your MySQL database. - Create your database login file as
db/login.php:
<?php
$hostname = '127.0.0.1';
$database = 's2756532_web_project';
$username = 'your_db_username';
$password = 'your_db_password';
?>- Ensure EMBOSS and Clustal Omega are installed and accessible in your
$PATH. - Set executable permissions on Bash and Python scripts if necessary.
- Start your web server and access
index.phpin your browser.
Use the web site to:
- Search protein sequences by name and taxon.
- Run Clustal Omega to align sequences and generate guide trees.
- Detect conserved motifs via EMBOSS
patmatmotifs. - View output as downloadable files and visual plots.
Try the live version here:
🌐 https://bioinfmsc8.bio.ed.ac.uk/~s2756532/web_project/index.php
Welcome page of the project:
Search page (glucose-6-phosphatase in Aves, top 10 sequences):
Results page (tree, matrix, plots, tables, downloads):
- 🔍 Search proteins by name and taxonomy
- 🧬 Run multiple sequence alignment (Clustal Omega)
- 🌳 Visualise guide trees interactively (jsPhyloSVG)
- 🎯 Detect conserved motifs (EMBOSS
patmatmotifs) - 📊 Generate custom plots: identity matrix, motif frequency (Python)
- 💾 Save and revisit past queries (user login)
- 🧪 Demo mode available (no login needed)
- Frontend: HTML, CSS, JavaScript (Raphael.js, jsPhyloSVG)
- Backend: PHP (with PDO), Bash scripts
- Database: MySQL
- Bioinformatics: Clustal Omega, EMBOSS, Biopython
- Plotting: Python (matplotlib, seaborn)
See full attribution and references on the site’s 📚 Statement of Credits
Main tools and libraries used:
AI assistance (ChatGPT) was used for debugging, scripting help, and layout suggestions — all reviewed and adapted.
🧾 This project was developed for educational purposes only. No commercial license is granted.
- Add BLAST support
- Allow multiple motif detection runs per session
- Improve mobile responsiveness
