Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jul 2;46(W1):W95-W101.
doi: 10.1093/nar/gky418.

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang  1 , Tanner Yohe  2 , Le Huang  1 , Sarah Entwistle  2 , Peizhi Wu  1 , Zhenglu Yang  1 , Peter K Busk  3 , Ying Xu  4 , Yanbin Yin  2
Affiliations

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al. Nucleic Acids Res. .

Abstract

Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
dbCAN is updated every year and now has 575 HMMs. X-axis: year; Y-axis: number of HMMs of families (blue) and subfamilies (red).
Figure 2.
Figure 2.
Overall design of dbCAN2 meta server. GCPU (gene cluster plot utility) and CGC-Finder (CAZyme gene cluster finder) are two tools developed for dbCAN2.
Figure 3.
Figure 3.
Comparison of annotation results for multi-domain CAZymes using three different tools. (A) Two example proteins (AT1G11720.1 and YP_002573728.1) are illustrated with their CAZyme domain architecture based on dbCAN search. (B) DIAMOND search result for the two proteins showing the best CAZy protein hit; (C) HMMER search result against dbCAN HMM database, from which (A) is derived; (D) Hotpep search result against PPR library; Frequency means the sum of conserved peptide frequencies and Hits means the number of conserved peptide hits (15).
Figure 4.
Figure 4.
Screenshots of dbCAN2 result pages. (A) Venn diagram to show overlaps among the results of the three tools; (B) CGC-Finder result tab; (C) Overview tab combining results from the three tools and SignalP; (D) genomic location plot of an example CGC (signature genes are in red, green and blue colors, while non-signature genes are in gray); (E) detailed information of an example CGC.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Cantarel B.L., Coutinho P.M., Rancurel C., Bernard T., Lombard V., Henrissat B.. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009; 37:D233–D238. - PMC - PubMed
    1. Ekstrom A., Taujale R., McGinn N., Yin Y.. PlantCAZyme: a database for plant carbohydrate-active enzymes. Database. 2014; 2014:bau079. - PMC - PubMed
    1. Huang L., Zhang H., Wu P., Entwistle E., Li X., Yohe T., Yi H., Yang Z., Yin Y.. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res. 2018; 46:D516–D521. - PMC - PubMed
    1. Yin Y., Mao X., Yang J., Chen X., Mao F., Xu Y.. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012; 40:W445–W451. - PMC - PubMed
    1. Cockburn D.W., Koropatkin N.M.. Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease. J. Mol. Biol. 2016; 428:3230–3252. - PubMed

Publication types