Class_project

This project has the codes and materials for the subfamily classification of a CAZyme family.

Project title: Subfamily classification and analysis of CAZy family

Goal: Classify the CAZy family into subfamilies, analyze and visualize them using Bioinformatics tools and methods.

In this tutorial, CAZy family GH31 was used to explain bioinformatics methods to analyze and visualize them.

Paper Link: A subfamily classification to choreograph the diverse activities within glycoside hydrolase family 31.
DOI: https://doi.org/10.1016/j.jbc.2023.103038

Steps involved and methods to identify the subfamily from a CAZy family:

1. Dataset and preprocess
2. Domain annotation using HMM and dbCAN
3. Extraction of modules (based on the annotation)
4. Construction of sequence similarity networks (SSN) using SSNpipe and analyzing SSNs based on characterized IDs from CAZy and EC numbers.
5. Visualization of SSN networks using Cytoscape
6. Phylogenentic analysis
7. Interpretation and discussion