Gene Isoform Finder

Projects Aim

The Gene Isoform Finder is a cutting-edge web application designed to easily find protein sequences (and all its isoforms) by searching a gene name. It simplifies the complex process to find patterns in protein sequences.

Search, and analyze gene isoform sequences from UniProt database. It integrates a powerful sequence search and pattern matching functionality, enabling to quickly identify specific patterns within the data.

Central to the application is the Plotly Dash Bio library, a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.

The Sequence Viewer component from Dash Bio, is offering fast, efficient pattern recognition and search capabilities. The application provides an intuitive interface for managing gene isoforms, ensuring ease of use while leveraging the advanced features of the Sequence Viewer component for in-depth analysis

Technologies and libraries

• Python 3.10.12
• Django 4.2.20
• Dash 2.18.2
• Dash Bio 1.0.2
• Plotly 6.0.0
• HTML.
• CSS.
• Bootstrap.

Project

1. Directory structure.

   All the project directories are named and explained in the next list. At the end of the list there is a structure tree image:

   • gene_isoform_finder: This is the main folder that contains the seq_viewer project, and the requirements.txt file.

     • seq_viewer: This is the project folder that contains the seq_viewer and the seq_viewer_app folders.

       • seq_viewer: Contains all the settings for the Django project.

       • seq_viewer_app: The Django app called Gene Isoform Finder. Contains all the front-end and back-end code for the Gene Isoform Finder application, following the Django project structure specifications.

         • migrations: Gene Isoform Finder model migrations.
         • static/ect_tool: Contains all the files for styling and event management for the Gene Isoform Finder. CSS, images, videos, JavaScript and Bootstrap files.
           • css: All CSS files for the Gene Isoform Finder style.
           • img: Predefined images for the Gene Isoform Finder views.
           • vendor: Folder containing Bootstrap, jQuery and jQuery-UI files.
         • templates/ect_tool: Contains all the HTML templates for the Gene Isoform Finder.

   • Directory tree structure:

     

2. Location of the main function.

   The main door or function of the project, is the ìndex() function from views.py file from 'gene_isoform_finder/seq_viewer/seq_viewer_app' folder.

3. How run the application.

   Install the packages needed using the requirements.txt file.

   pip install -r requirements.txt

   Clone the repository.

   git clone git@github.com:XLlobet/gene_isoform_finder.git
   cd gene_isoform_finder/seq_viewer

   Run the application:

   python3 manage.py migrate
   python3 manage.py runserver

   Visite the app in your brouser at http://127.0.0.1:8000/