A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database
Thousands of plasmid sequences are now publicly available in the NCBI nucleotide database, but they are not reliably annotated to distinguish complete plasmids from plasmid fragments, such as gene or contig sequences; therefore, retrieving complete plasmids for downstream analyses is challenging. He...
Main Authors: | , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2017-06-01
|
Series: | Data in Brief |
Subjects: | |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340917301567 |
id |
doaj-1d6c9918af444a369681cdd12458e5a8 |
---|---|
record_format |
Article |
spelling |
doaj-1d6c9918af444a369681cdd12458e5a82020-11-25T02:12:28ZengElsevierData in Brief2352-34092017-06-0112C42342610.1016/j.dib.2017.04.024A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide databaseAlex Orlek0Hang Phan1Anna E. Sheppard2Michel Doumith3Matthew Ellington4Tim Peto5Derrick Crook6A. Sarah Walker7Neil Woodford8Muna F. Anjum9Nicole Stoesser10Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKAntimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UKNIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKNIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UKNIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UKNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UKThousands of plasmid sequences are now publicly available in the NCBI nucleotide database, but they are not reliably annotated to distinguish complete plasmids from plasmid fragments, such as gene or contig sequences; therefore, retrieving complete plasmids for downstream analyses is challenging. Here we present a curated dataset of complete bacterial plasmids from the clinically relevant Enterobacteriaceae family. The dataset was compiled from the NCBI nucleotide database using curation steps designed to exclude incomplete plasmid sequences, and chromosomal sequences misannotated as plasmids. Over 2000 complete plasmid sequences are included in the curated plasmid dataset. Protein sequences produced from translating each complete plasmid nucleotide sequence in all 6 frames are also provided. Further analysis and discussion of the dataset is presented in an accompanying research article: “Ordering the mob: insights into replicon and MOB typing…” (Orlek et al., 2017) [1]. The curated plasmid sequences are publicly available in the Figshare repository.http://www.sciencedirect.com/science/article/pii/S2352340917301567PlasmidsSequence data curationComplete genomesEnterobacteriaceae family |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Alex Orlek Hang Phan Anna E. Sheppard Michel Doumith Matthew Ellington Tim Peto Derrick Crook A. Sarah Walker Neil Woodford Muna F. Anjum Nicole Stoesser |
spellingShingle |
Alex Orlek Hang Phan Anna E. Sheppard Michel Doumith Matthew Ellington Tim Peto Derrick Crook A. Sarah Walker Neil Woodford Muna F. Anjum Nicole Stoesser A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database Data in Brief Plasmids Sequence data curation Complete genomes Enterobacteriaceae family |
author_facet |
Alex Orlek Hang Phan Anna E. Sheppard Michel Doumith Matthew Ellington Tim Peto Derrick Crook A. Sarah Walker Neil Woodford Muna F. Anjum Nicole Stoesser |
author_sort |
Alex Orlek |
title |
A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |
title_short |
A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |
title_full |
A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |
title_fullStr |
A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |
title_full_unstemmed |
A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |
title_sort |
curated dataset of complete enterobacteriaceae plasmids compiled from the ncbi nucleotide database |
publisher |
Elsevier |
series |
Data in Brief |
issn |
2352-3409 |
publishDate |
2017-06-01 |
description |
Thousands of plasmid sequences are now publicly available in the NCBI nucleotide database, but they are not reliably annotated to distinguish complete plasmids from plasmid fragments, such as gene or contig sequences; therefore, retrieving complete plasmids for downstream analyses is challenging. Here we present a curated dataset of complete bacterial plasmids from the clinically relevant Enterobacteriaceae family. The dataset was compiled from the NCBI nucleotide database using curation steps designed to exclude incomplete plasmid sequences, and chromosomal sequences misannotated as plasmids. Over 2000 complete plasmid sequences are included in the curated plasmid dataset. Protein sequences produced from translating each complete plasmid nucleotide sequence in all 6 frames are also provided. Further analysis and discussion of the dataset is presented in an accompanying research article: “Ordering the mob: insights into replicon and MOB typing…” (Orlek et al., 2017) [1]. The curated plasmid sequences are publicly available in the Figshare repository. |
topic |
Plasmids Sequence data curation Complete genomes Enterobacteriaceae family |
url |
http://www.sciencedirect.com/science/article/pii/S2352340917301567 |
work_keys_str_mv |
AT alexorlek acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT hangphan acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT annaesheppard acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT micheldoumith acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT matthewellington acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT timpeto acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT derrickcrook acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT asarahwalker acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT neilwoodford acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT munafanjum acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT nicolestoesser acurateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT alexorlek curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT hangphan curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT annaesheppard curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT micheldoumith curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT matthewellington curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT timpeto curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT derrickcrook curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT asarahwalker curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT neilwoodford curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT munafanjum curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase AT nicolestoesser curateddatasetofcompleteenterobacteriaceaeplasmidscompiledfromthencbinucleotidedatabase |
_version_ |
1724909102533967872 |