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Cited by 1,793

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

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

Open access
Yin, Yanbin, Mao, Xizeng, Yang, Jincai, Chen, Xin, Mao, Fenglou, Xu, Ying·2012·Nucleic Acids Research
DOI 10.1093/nar/gks479
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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.

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Research works printed but not linked: 22

  1. Cantarel, 2009, The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Res., 37, D233, 10.1093/nar/gkn663 · DOI · Paper page
  2. Li, 2009, Bioprospecting metagenomes: glycosyl hydrolases for converting biomass, Biotechnol. Biofuels, 2, 10, 10.1186/1754-6834-2-10 · DOI · Paper page
  3. Tasse, 2010, Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes, Genome Res., 20, 1605, 10.1101/gr.108332.110 · DOI · Paper page
  4. Allgaier, 2010, Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community, PloS One, 5, e8812, 10.1371/journal.pone.0008812 · DOI · Paper page
  5. Hess, 2011, Metagenomic discovery of biomass-degrading genes and genomes from cow rumen, Science, 331, 463, 10.1126/science.1200387 · DOI · Paper page
  6. Park, 2010, CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database, Glycobiology, 20, 1574, 10.1093/glycob/cwq106 · DOI · Paper page
  7. Zhu, 2011, Evidence of cellulose metabolism by the giant panda gut microbiome, Proc. Natl Acad Sci USA, 108, 17714, 10.1073/pnas.1017956108 · DOI · Paper page
  8. Duplessis, 2011, Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proc. Natl Acad. Sci. USA, 108, 9166, 10.1073/pnas.1019315108 · DOI · Paper page
  9. Brulc, 2009, Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases, Proc. Natl Acad. Sci. USA, 106, 1948, 10.1073/pnas.0806191105 · DOI · Paper page
  10. Finn, 2006, Pfam: clans, web tools and services, Nucleic Acids Res., 34, D247, 10.1093/nar/gkj149 · DOI · Paper page
  11. Hunter, 2009, InterPro: the integrative protein signature database, Nucleic Acids Res., 37, D211, 10.1093/nar/gkn785 · DOI · Paper page
  12. Marchler-Bauer, 2009, CDD: specific functional annotation with the Conserved Domain Database, Nucleic Acids Res., 37, D205, 10.1093/nar/gkn845 · DOI · Paper page
  13. Bayer, 2008, From cellulosomes to cellulosomics, Chem. Rec., 8, 364, 10.1002/tcr.20160 · DOI · Paper page
  14. Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198 · DOI · Paper page
  15. Handelsman, 2004, Metagenomics: application of genomics to uncultured microorganisms, Microbiol. Mol. Biol. Rev., 68, 669, 10.1128/MMBR.68.4.669-685.2004 · DOI · Paper page
  16. Fernandez-Arrojo, 2010, Metagenomic era for biocatalyst identification, Curr. Opin. Biotechnol., 21, 725, 10.1016/j.copbio.2010.09.006 · DOI · Paper page
  17. Lee, 2010, Approaches for novel enzyme discovery from marine environments, Curr. Opin. Biotechnol., 21, 353, 10.1016/j.copbio.2010.01.015 · DOI
  18. Godzik, 2011, Metagenomics and the protein universe, Curr. Opin. Struct. Biol., 21, 398, 10.1016/j.sbi.2011.03.010 · DOI
  19. Markowitz, 2010, The integrated microbial genomes system: an expanding comparative analysis resource, Nucleic Acids Res., 38, D382, 10.1093/nar/gkp887 · DOI · Paper page
  20. Yooseph, 2007, The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families, PLoS Biol., 5, e16, 10.1371/journal.pbio.0050016 · DOI · Paper page
  21. Seshadri, 2007, CAMERA: a community resource for metagenomics, PLoS Biol., 5, e75, 10.1371/journal.pbio.0050075 · DOI · Paper page
  22. Kennedy, 2008, Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments, Microb. Cell Fact, 7, 27, 10.1186/1475-2859-7-27 · DOI · Paper page

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Metadata

Authors
Yin, Y., Mao, X., Yang, J., Chen, X., Mao, F., & Xu, Y.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2012-05-29
Volume
40
Issue
W1
Pages
W445-W451
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gks479
OpenAlex
W2103539617
Cited by
1,793
References
3
FWCI
16.38
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by-nc/3.0 (vor, 1590 d)

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CoChat. (2026). Citation check: dbCAN: a web resource for automated carbohydrate-active enzyme annotation. https://app.cochat.ai/papers/10.1093/nar/gks479
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Yin, Y., Mao, X., Yang, J., Chen, X., Mao, F., & Xu, Y. (2012). dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Research. https://doi.org/10.1093/nar/gks479

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