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dbCAN3: automated carbohydrate-active enzyme and substrate annotation

Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recyc...

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Autores principales: Zheng, Jinfang, Ge, Qiwei, Yan, Yuchen, Zhang, Xinpeng, Huang, Le, Yin, Yanbin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320055/
https://www.ncbi.nlm.nih.gov/pubmed/37125649
http://dx.doi.org/10.1093/nar/gkad328
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author Zheng, Jinfang
Ge, Qiwei
Yan, Yuchen
Zhang, Xinpeng
Huang, Le
Yin, Yanbin
author_facet Zheng, Jinfang
Ge, Qiwei
Yan, Yuchen
Zhang, Xinpeng
Huang, Le
Yin, Yanbin
author_sort Zheng, Jinfang
collection PubMed
description Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.
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spelling pubmed-103200552023-07-06 dbCAN3: automated carbohydrate-active enzyme and substrate annotation Zheng, Jinfang Ge, Qiwei Yan, Yuchen Zhang, Xinpeng Huang, Le Yin, Yanbin Nucleic Acids Res Web Server Issue Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction. Oxford University Press 2023-05-01 /pmc/articles/PMC10320055/ /pubmed/37125649 http://dx.doi.org/10.1093/nar/gkad328 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Zheng, Jinfang
Ge, Qiwei
Yan, Yuchen
Zhang, Xinpeng
Huang, Le
Yin, Yanbin
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title_full dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title_fullStr dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title_full_unstemmed dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title_short dbCAN3: automated carbohydrate-active enzyme and substrate annotation
title_sort dbcan3: automated carbohydrate-active enzyme and substrate annotation
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320055/
https://www.ncbi.nlm.nih.gov/pubmed/37125649
http://dx.doi.org/10.1093/nar/gkad328
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