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

Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter Kamp Busk, Ying Xu, Yanbin Yin

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

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.
OriginalsprogEngelsk
TidsskriftNucleic Acids Research
Vol/bind46
Udgave nummerW1
Sider (fra-til)W95-W101
ISSN0305-1048
DOI
StatusUdgivet - jul. 2018

Citer dette

Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., ... Yin, Y. (2018). dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 46(W1), W95-W101. https://doi.org/10.1093/nar/gky418
Zhang, Han ; Yohe, Tanner ; Huang, Le ; Entwistle, Sarah ; Wu, Peizhi ; Yang, Zhenglu ; Busk, Peter Kamp ; Xu, Ying ; Yin, Yanbin. / dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. I: Nucleic Acids Research. 2018 ; Bind 46, Nr. W1. s. W95-W101.
@article{b3a0bd9dbc7b4e00873a34e93cb676a9,
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.",
author = "Han Zhang and Tanner Yohe and Le Huang and Sarah Entwistle and Peizhi Wu and Zhenglu Yang and Busk, {Peter Kamp} and Ying Xu and Yanbin Yin",
year = "2018",
month = "7",
doi = "10.1093/nar/gky418",
language = "English",
volume = "46",
pages = "W95--W101",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "W1",

}

Zhang, H, Yohe, T, Huang, L, Entwistle, S, Wu, P, Yang, Z, Busk, PK, Xu, Y & Yin, Y 2018, 'dbCAN2: a meta server for automated carbohydrate-active enzyme annotation', Nucleic Acids Research, bind 46, nr. W1, s. W95-W101. https://doi.org/10.1093/nar/gky418

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. / Zhang, Han; Yohe, Tanner; Huang, Le; Entwistle, Sarah; Wu, Peizhi; Yang, Zhenglu; Busk, Peter Kamp; Xu, Ying; Yin, Yanbin.

I: Nucleic Acids Research, Bind 46, Nr. W1, 07.2018, s. W95-W101.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

AU - Zhang, Han

AU - Yohe, Tanner

AU - Huang, Le

AU - Entwistle, Sarah

AU - Wu, Peizhi

AU - Yang, Zhenglu

AU - Busk, Peter Kamp

AU - Xu, Ying

AU - Yin, Yanbin

PY - 2018/7

Y1 - 2018/7

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gky418

DO - 10.1093/nar/gky418

M3 - Journal article

VL - 46

SP - W95-W101

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -

Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research. 2018 jul;46(W1):W95-W101. https://doi.org/10.1093/nar/gky418