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Protocols

Enterobase specifications

Information


Unique identifier OMICS_23752
Name Enterobase
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 1.1.2
Maintained Yes

Documentation


Maintainers


  • person_outline Zhemin Zhou
  • person_outline Martin Sergeant
  • person_outline Nabil-Fareed Alikhan

Additional information


https://bitbucket.org/enterobase/enterobase-web/wiki/Basic%20usage%20of%20Grapetree%20tutorial https://bitbucket.org/enterobase/enterobase-web/wiki/species-index

Publication for Enterobase

Enterobase citations

 (28)
library_books

Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms

2018
PLoS One
PMCID: 5931505
PMID: 29718935
DOI: 10.1371/journal.pone.0195537

[…] nomes comprising 13 E. coli pathotypes (Table B in ). The taxonomic and phenotypic identifications were based on the latest published data[]. E. coli strain pathogroup assignment was according to the EnteroBase database freely available at https://enterobase.warwick.ac.ukProblem Definition and Notation. Given a set B of bacteria, a subset B of B, and a set of orthologous proteins P, we want to fin […]

library_books

A genomic overview of the population structure of Salmonella

2018
PLoS Genet
PMCID: 5886390
PMID: 29621240
DOI: 10.1371/journal.pgen.1007261

[…] s genomic contigs from the short reads within 2 hours and calculates MLST assignments from those genomes at the levels of legacy MLST, ribosomal gene MLST (rMLST) [], soft cgMLST, and wgMLST (; ) []. EnteroBase also supports calling SNPs from up to 1,000 genomes against a reference genome as well as the graphic evaluation of genetic relationships between entries. Here, we re-examine the population […]

library_books

Multidrug Resistant Salmonella enterica 4,[5],12:i: Sequence Type 34, New South UK, Australia, 2016–2017

2018
PMCID: 5875280
PMID: 29553318
DOI: 10.3201/eid2404.171619

[…] bricate). Markers of colistin resistance were examined by using CLC Genomics Workbench (QIAGEN, Valencia, CA, USA). We identified Salmonella 4,[5],12:i:- genomes recovered in Europe and Asia by using Enterobase (https://enterobase.warwick.ac.uk/). We confirmed phenotypic resistance on a randomly selected subset of isolates by using the BD Phoenix system (Becton Dickinson, Franklin Lakes, NJ, USA) […]

library_books

Impact of human associated Escherichia coli clonal groups in Antarctic pinnipeds: presence of ST73, ST95, ST141 and ST131

2018
Sci Rep
PMCID: 5856829
PMID: 29549276
DOI: 10.1038/s41598-018-22943-0

[…] ed in Enterobase using the MSTree V2 algorithm and the cgMLST v1 scheme. This scheme consists of 2,513 genes that were present in over 98% of 3,457 genomes, which represented most of the diversity in Enterobase at the time (May 2016) https://bitbucket.org/enterobase/enterobase-web/wiki/Escherichia%20Statistics. Antimicrobial resistances, plasmid detection and typing were in silico determined by us […]

library_books

A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST 1974

2018
Microb Genom
PMCID: 5885013
PMID: 29509137
DOI: 10.1099/mgen.0.000161

[…] o the EnteroBase, which performs a pipeline of assembly, annotation and several in silico typing schemes, including Achtman 7 gene multilocus sequence typing (MLST) and ribosomal MLST (rMLST) (http://enterobase.warwick.ac.uk).For the selection of the genomes to include in the phylogenetic analysis, we obtained the total list of rMLST representatives (provided by EnteroBase in the public workspace […]

call_split

Complete Genome Sequence of a Ciprofloxacin Resistant Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State

2018
Genome Announc
PMCID: 5834327
PMID: 29496839
DOI: 10.1128/genomeA.00125-18
call_split See protocol

[…] Process 2 (HGAP 2) workflow to obtain a 4,900,326-bp circularized consensus sequence, with 52.2% GC content. The serovar designation and multilocus sequence type (MLST) were confirmed in silico using EnteroBase (https://enterobase.warwick.ac.uk/species/index/senterica) and SISTR (), respectively. The NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok) […]

Citations

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Enterobase institution(s)
Warwick Medical School, University of Warwick, Coventry, UK; Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal; Universidade de Lisboa, Faculdade de Medicina, Instituto de Microbiologia and Instituto de Medicina Molecular, Lisboa, Portugal; Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
Enterobase funding source(s)
Supported by grant (BBSRC BB/L020319/1).

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