Paper Info
Title
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
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.
Year
DOI
Venue
2018
10.1093/nar/gky418
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Enzyme,Cysteine,Annotation,Biology,Biochemistry,Genetics,Carbohydrate metabolism,Carbohydrate
Journal
46
Issue
ISSN
Citations 
W1
0305-1048
0
PageRank 
References 
Authors
0.34
10
9
Name
Order
Citations
PageRank
Han Zhang112328.55
Tanner Yohe200.34
Le Huang321.73
Sarah Entwistle420.71
Peizhi Wu583.52
Zhenglu Yang625735.45
Peter K. Busk761.07
Ying Xu852861.00
Yanbin Yin9317.75