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

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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 languageEnglish
    Pages (from-to)D320-D324
    Number of pages5
    JournalNucleic Acids Research
    Volume45
    Issue numberD1
    DOIs
    Publication statusPublished - 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

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