• probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

    • Daniel Greuter
      Department für Mikrobiologie und Ökosystemforschung, Fakultät für Lebenswissenschaften, Universität Wien
    • Alexander Loy
      Department für Mikrobiologie und Ökosystemforschung, Fakultät für Lebenswissenschaften, Universität Wien
    • Matthias Horn
      Department für Mikrobiologie und Ökosystemforschung, Fakultät für Lebenswissenschaften, Universität Wien
    • Thomas Rattei
      Department für Mikrobiologie und Ökosystemforschung, Fakultät für Lebenswissenschaften, Universität Wien
  • probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.

  • PDF

  • http://phaidra.univie.ac.at/o:930761

  • Wissenschaftlicher Artikel

  • Veröffentlichte Version

  • Nucleic Acids Research

  • 2015

  • 44

  • D1

  • Oxford University Press (OUP)

  • Englisch

  • Frei zugänglich

  • CC BY Namensnennung 4.0 International
    © The Author(s) 2015

  • P25111-B22 – Fonds zur Förderung der wissenschaftlichen Forschung (FWF)

  • I2320-B22 – Fonds zur Förderung der wissenschaftlichen Forschung (FWF)

  • I1628-B22 – Fonds zur Förderung der wissenschaftlichen Forschung (FWF)

  • LS12-001 – Wiener Wissenschafts-, Forschungs- und Technologiefonds (WWTF)

  • StG EVOCHLAMY, 281633 – Europäische Union (alle Programme)

  • 0305-1048