TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Liam D. H. Elbourne; Sasha G. Tetu; Karl A. Hassan; Ian T. Paulsen

doi:10.1093/nar/gkw1068

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Liam D. H. Elbourne, Sasha G. Tetu, Karl A. Hassan, Ian T. Paulsen

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229 Citations (Scopus)

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Abstract

All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.

Original language	English
Pages (from-to)	D320-D324
Number of pages	5
Journal	Nucleic Acids Research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw1068
Publication status	Published - 4 Jan 2017

Bibliographical note

Copyright the Author(s) 2016. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

CLASSIFICATION-SYSTEM
EUKARYOTES

Access to Document

10.1093/nar/gkw1068

Publisher version (open access)Final published version, 1.72 MBLicence: CC BY-NC

Cite this

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title = "TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life",

abstract = "All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.",

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AU - Paulsen, Ian T.

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AB - All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.

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TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Abstract

Bibliographical note

Keywords

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Toxic Oceans: how do anthropogenic pollutants impact vital marine microbes?

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TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

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Projects

Toxic Oceans: how do anthropogenic pollutants impact vital marine microbes?

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