Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies (Q39073976)

27 February 2018

title

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies (English)

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27 February 2018

main subject

database

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whole genome sequencing

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Seok-Hwan Yoon

1

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27 February 2018

Sung-Min Ha

2

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27 February 2018

Soonjae Kwon

3

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27 February 2018

Jeongmin Lim

4

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27 February 2018

Yeseul Kim

5

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27 February 2018

Hyungseok Seo

6

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27 February 2018

Jongsik Chun

7

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27 February 2018

language of work or name

English

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publication date

22 December 2016

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27 February 2018

International Journal of Systematic and Evolutionary Microbiology

published in

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27 February 2018

volume

67

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27 February 2018

page(s)

1613-1617

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27 February 2018

issue

5

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27 February 2018

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Ribosomal Database Project: data and tools for high throughput rRNA analysis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Search and clustering orders of magnitude faster than BLAST

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Shifting the genomic gold standard for the prokaryotic species definition

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Application of tetranucleotide frequencies for the assignment of genomic fragments

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Optimal alignments in linear space

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

Use of recA as an alternative phylogenetic marker in the family Vibrionaceae

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5563544

21 August 2018

Identifiers

DOI

10.1099/IJSEM.0.001755

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27 February 2018

PMCID

5563544

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27 February 2018

PubMed ID

28005526

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27 February 2018