Complex programs can fail to deliver their results without an adequate visualization interface. FlaGs (Flanking Genes) is a bioinformatics tool that detects homologous gene clusters and outputs a graphical visualization along with a phylogenetic tree. Recent updates to the FlaGs algorithm has made this tool domain-aware, however it is lacking the visual interface to support such feature.
Project aims:
| Aim | Imporve | How | Library/Framework |
|---|---|---|---|
| 1 | New visualisation code that does not crash the program when running it display-less | Rewrite the visualisation code | Matplotlib |
| 2 | Accommodate graphical output for a domain-aware FlaGs | Display domains inside proteins. Preferably output in a .HTML file | Plotly |
| 3 | Need for a fully interactive domain-aware FlaGs | Build an application/dashboard | Plotly Dash |
Overview of repository files including the script and each files it requires in a share directory. All files were acquired using FlaGs2, https://github.com/GCA-VH-lab/FlaGs2
Downloading the script with its corresponding file/s in a shared directory should be enough to run and display the results locally. Some dependencies, such as dash_bio might need to be downloaded in order to run the interactive_dash.py script.
How to run
| Step | Script | Run with command | Comments |
|---|---|---|---|
| 1 | Installing Requirements | sudo pip install -r requirements.txt | Install all necessary modules |
| 2 | Matplotlib visualisation | python3 ./image.py | Can be run without step 1 if matplotlib is already installed |
| 3 | Semi-interactive | python3 ./semi-interactive_html.py | HTML file opens in a werbrowser tab |
| 4 | Interactive app | python3 ./interactive_html.py | App still not deplyed, open this link (http://127.0.0.1:8050/) to view the app |
- The matplotlib.py script bypasses some limitations the FlaGs1 visualization had. This script is already incorporated in the follow-up version, FlaGs2.
- The semi-interactive_html.py script allows the user to visualize domains inside the genes as discovered by the domains search option of FlaGs2. It allows limited interactivity whereby the user can toggle domains and proteins using the legend on the right-hand side. Given the simplicity and limitations to this layout, it is recommended to use a limited number of domains per proteins (e.g. 3-4 domains). This is because using more makes the legend less convenient for use due to its length.
- The full interactive_dash.py script allows full interactivity and access to all domains regardless of the number of domains. It includes a domain plot which is created upon the selection of a gene as well as a sequence alignment of the query proteins sequences (black arrows) aligned with the MAFFT multiple sequence alignment method.
This project was made to improve the bioinformatic tool FlaGs developed by the Atkinson-Hauryliuk lab, https://github.com/GCA-VH-lab.