Open Access
International Journal of Systematic and Evolutionary Microbiology, volume 67, issue 5, pages 1613-1617
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
Yoon Seok Jun
1
,
Ha Sung Kyu
1
,
Kwon Soon-Jae
1
,
Lim Jeongmin
1
,
Kim Yeseul
1
,
Seo Hyungseok
1
,
Chun Jongsik
1
1
Department of ChunLab, Inc, Seoul National University, Seoul, Republic of Korea
|
Publication type: Journal Article
Publication date: 2016-12-22
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor: 2.8
ISSN: 14665026, 14665034
PubMed ID:
28005526
General Medicine
Microbiology
Ecology, Evolution, Behavior and Systematics
Abstract
The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
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- We do not take into account publications that without a DOI.
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Yoon S. J. et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies // International Journal of Systematic and Evolutionary Microbiology. 2016. Vol. 67. No. 5. pp. 1613-1617.
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Yoon S. J., Ha S. K., Kwon S., Lim J., Kim Y., Seo H., Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies // International Journal of Systematic and Evolutionary Microbiology. 2016. Vol. 67. No. 5. pp. 1613-1617.
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TY - JOUR
DO - 10.1099/ijsem.0.001755
UR - https://doi.org/10.1099%2Fijsem.0.001755
TI - Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
T2 - International Journal of Systematic and Evolutionary Microbiology
AU - Yoon, Seok Jun
AU - Ha, Sung Kyu
AU - Kwon, Soon-Jae
AU - Lim, Jeongmin
AU - Kim, Yeseul
AU - Seo, Hyungseok
AU - Chun, Jongsik
PY - 2016
DA - 2016/12/22 00:00:00
PB - Microbiology Society
SP - 1613-1617
IS - 5
VL - 67
PMID - 28005526
SN - 1466-5026
SN - 1466-5034
ER -
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@article{2016_Yoon,
author = {Seok Jun Yoon and Sung Kyu Ha and Soon-Jae Kwon and Jeongmin Lim and Yeseul Kim and Hyungseok Seo and Jongsik Chun},
title = {Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies},
journal = {International Journal of Systematic and Evolutionary Microbiology},
year = {2016},
volume = {67},
publisher = {Microbiology Society},
month = {dec},
url = {https://doi.org/10.1099%2Fijsem.0.001755},
number = {5},
pages = {1613--1617},
doi = {10.1099/ijsem.0.001755}
}
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MLA
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Yoon, Seok Jun, et al. “Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.” International Journal of Systematic and Evolutionary Microbiology, vol. 67, no. 5, Dec. 2016, pp. 1613-1617. https://doi.org/10.1099%2Fijsem.0.001755.