dbCAN protocols

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dbCAN specifications

Information


Unique identifier OMICS_29849
Name dbCAN
Alternative name dbCAN2
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Output format TXT
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yanbin Yin <>

Additional information


An old version of dbCAN is available at: http://csbl.bmb.uga.edu/dbCAN/blast.php

Publication for dbCAN

dbCAN in pipelines

 (32)
2018
PMCID: 5767910
PMID: 29349107
DOI: 10.1016/j.dib.2017.12.060

[…] search (blast version 2.2.31) against the ncbi nr database (update 02/2016). for functional annotation, blast search results were analyzed with blast2go version 4.1 . cazymes were identified with dbcan version 5.0 . proteins predicted to contain a signal peptide by both signalp version 4.1 and targetp version 1.1 were categorized as secreted proteins. proteases were identified by homology […]

2018
PMCID: 5849685
PMID: 29535379
DOI: 10.1038/s41467-018-03366-x

[…] website. the genetic neighborhood surrounding identified candidate agarases were then systematically characterized using artemis. identified orfs were trimmed, exported, and annotated manually using dbcan and blastp. to determine the putative region of insertion of the ag-pul into the ancestral bu chromosome, the non-agarolytic strain bu atcc 8492 was used as a sequenced referenced genome. […]

2018
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] was conducted by cafe with lambda 0.314, p value 0.01 and 1000 random samples []., putative cazymes were identified using the hmmer 3.1b1 with annotated hmm profiles of cazymes downloaded from the dbcan database []. the identification and classification of the membrane transporters superfamily were obtained by using blastp searches with e value <1e-5 and identity > 40% […]

2017
PMCID: 5428652
PMID: 28352091
DOI: 10.1038/s41598-017-00567-0

[…] the hmmsearch program in the hmmer 3.1b2 package (http://hmmer.org/), was used to search all predicted proteomes with the family-specific hidden markov model profiles of cazymes from the dbcan database. primary results were processed with an e-value threshold of 1e-7. protein kinases and phosphatases were detected using hmmsearch based on the eukaryotic kinase and phosphatase […]

2017
PMCID: 5480151
PMID: 28649277
DOI: 10.1186/s13068-017-0840-y

[…] lyases (pls) and glycosyltransferases (gts) in the cazy database (http://www.cazy.org) []. the identified cazymes were analyzed for carbohydrate-binding domains (cbms) and dockerin domains using dbcan []. a blastp was performed for all identified cazymes using the ncbi nr database (http://blast.ncbi.nlm.nih.gov/blast.cgi) to identify the closest related known protein, and blastp was also […]

dbCAN in publications

 (234)
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] was conducted by cafe with lambda 0.314, p value 0.01 and 1000 random samples []., putative cazymes were identified using the hmmer 3.1b1 with annotated hmm profiles of cazymes downloaded from the dbcan database []. the identification and classification of the membrane transporters superfamily were obtained by using blastp searches with e value <1e-5 and identity > 40% […]

PMCID: 5943477
PMID: 29774012
DOI: 10.3389/fmicb.2018.00839

[…] renamed to ‘ph’ in the current study., carbohydrate active enzymes and sulfatases were identified in the p. hydrolytica s66t genome using hidden markov model searches against local versions of the dbcan 5.0 () and pfam () databases. predicted protein sequences were compared with homologs at ncbi using blastp searches against the pdb and nr databases. sulfatase homologs were also compared […]

PMCID: 5934417
PMID: 29755442
DOI: 10.3389/fmicb.2018.00826

[…] and genomes (kegg) (kanehisa and goto, ). fisher's exact test was used to obtain enriched functional terms (p < 0.05). genes encoding lignocellulose-active enzymes were further annotated via dbcan (lepoivre et al., ; yin et al., )., real-time quantitative pcr was used to verify the gene expression level calculated from rna-seq data. a few arbitrarily selected lignocellulose-active enzyme […]

PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] secretomes in aspergillus species were annotated with information on protein family from pfam database (http://pfam.xfam.org/) and carbohydrate-binding modules from cazy (http://www.cazy.org/) and dbcan v5.0 (http://csbl.bmb.uga.edu/dbcan/) databases using hmmpress and hmmscan utilities in hmmer3 (http://hmmer.org/) with profile-specific ga (gathering) thresholds. furthermore, the predicted […]

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] enzymes (cazymes) were identified by scanning using hmmer 3.0 against the hidden markov model (hmms) corresponding to the pfam cazyme family and subfamily (download from http://csbl.bmb.uga.edu/dbcan/). secondary metabolism genes were annotated based on their genomic context and domain content using an automatic web-based software smurf (www.jcvi.org/smurf/)., the gene families of potential […]

dbCAN institution(s)
College of Computer and Control Engineering, Nankai University, Tianjin, China; Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA; Department of Science and Environment, Roskilde University, Roskilde, Denmark; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
dbCAN funding source(s)
Supported by the National Science Foundation (NSF) CAREER award [DBI-1652164]; National Institutes of Health (NIH) AREA award [1R15GM114706]; Research & Artistry Award of the NIU [2017-YIN]; National Natural Science Foundation of China [31728013].

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