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

By Yanbin Yin, Xizeng Mao, Jincai Yang, Xin Chen, Fenglou Mao, Ying Xu. 2012

1,626 citations recorded by the source corpus.

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.

Subfields: Biomedical Engineering, Biotechnology, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biomedical Engineering

In Biotechnology

In Molecular Biology

Citations in the corpus

Gut Microbiota-Targeted Diets Modulate Human Immune Status (2020, positive): “11) (Yin et al., 2012; Huang et al., 2018) on genes called from FragGeneScan (Rho et al.”
The carbohydrate-active enzymes database (CAZy) in 2013 (2013, background): “In this respect, one should note that the correspondence between CAZy families and those in PFAM (16)/INTERPRO (17) or DBCAN (18) is far from perfect.”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, methodology): “binned genomes and the two Sorangium cellulosum strains were extracted using dbCAN [28], which was based on the protein families generated by CAZy database (http://www.”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “Carbohydrate-active enzyme annotations as defined by CAZy (25) were generated using the dbCAN HMM models (26).”
U.S. immigration westernizes the human gut microbiome (2018, methodology): “In order to better understand the substrates degraded by these pathways that are either lost or below the detection limit in US immigrants, we assembled the shotgun data into scaffolds and annotated carbohydratedegrading enzymes (CAZymes) (Lombard et al., 2014; Yin et al., 2012).”
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation (2018, background): “In addition to their significance in bioenergy and agricultural industries (4), CAZymes are also extremely important for human health (5).”