A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database

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...

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Main Authors: 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
Format: Article
Language:English
Published: Elsevier 2017-06-01
Series:Data in Brief
Subjects:
Plasmids
Sequence data curation
Complete genomes
Enterobacteriaceae family
Online Access:http://www.sciencedirect.com/science/article/pii/S2352340917301567
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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
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