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Nucleic Acids Res. 2017 Jan 4;45(D1):D320-D324. doi: 10.1093/nar/gkw1068. Epub 2016 Nov 28.

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

Author information

1
Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia liam.elbourne@mq.edu.au.
2
Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia.
3
Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia ian.paulsen@mq.edu.au.

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.

PMID:
27899676
PMCID:
PMC5210551
DOI:
10.1093/nar/gkw1068
[Indexed for MEDLINE]
Free PMC Article

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