dbCAN: a web resource for automated carbohydrate-active enzyme annotation

TLDR

Carbohydrate‑active enzymes (CAZymes) are essential to biotechnology, especially biofuels, because they synthesize, degrade, and modify all terrestrial carbohydrates. The authors created dbCAN, a web tool that automatically annotates CAZyme domains in any protein dataset, such as those from newly sequenced genomes. dbCAN defines a signature domain for each CAZyme family using CDD searches and literature curation, then builds hidden Markov models for these domains to perform the annotation. The family‑specific HMMs constitute the core contribution and enable the automated CAZyme annotation performed by dbCAN.

Abstract

Carbohydrate-active enzymes (CAZymes) are very important to the biotech industry, particularly the emerging biofuel industry because CAZymes are responsible for the synthesis, degradation and modification of all the carbohydrates on Earth. We have developed a web resource, dbCAN (http://csbl.bmb.uga.edu/dbCAN/annotate.php), to provide a capability for automated CAZyme signature domain-based annotation for any given protein data set (e.g. proteins from a newly sequenced genome) submitted to our server. To accomplish this, we have explicitly defined a signature domain for every CAZyme family, derived based on the CDD (conserved domain database) search and literature curation. We have also constructed a hidden Markov model to represent the signature domain of each CAZyme family. These CAZyme family-specific HMMs are our key contribution and the foundation for the automated CAZyme annotation.