CAZy Database Parser

This is a series of scripts that parse and extract information about each carbohydrate binding module (CBM) family from the Carbohydrate Active enZYme Database.

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What is the Carbohydrate Active enZYme Database?

CAZy is an online database created in 1998 that holds genomic, structural and biochemical information about Carbohydrate-Active Enzymes (CAZymes) and their associated modules.

These include:

• Glycoside Hydrolases (GH)
• GlycosylTransferases (GT)
• Polysaccharide Lyases (PL)
• Carbohydrate Esterases (CE)
• Auxilliary Activities (AA)
• Carbohydrate Binding Modules (CBM)

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Included Scripts

cazy_parse.py

Consolidates the 'Activity in Family' information from each CBM page into a single excel file. 'Note' information is used in place of 'Activity in Family' if that field is not populated.

database_trim.py

Downloads and extracts each CBM listed in the CAZy database across bacteria, archaea, viruses and eukaryota.

cazy_functions.py

Generic functions used across the other scripts.

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Dependencies

• pandas 1.5.2
• python3-wget 3.2

Written in Python 3.10.9