title: probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.
abstract: 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.
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria.
authors.forename: Daniel
authors.initials: D
authors.lastname: Greuter
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria loy@microbial-ecology.net.
authors.forename: Alexander
authors.initials: A
authors.lastname: Loy
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria horn@microbial-ecology.net.
authors.forename: Matthias
authors.initials: M
authors.lastname: Horn
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
mesh_terms: D003198:Computer Simulation; D017931:DNA Primers / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D020407:Internet; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry*; D017423:Sequence Analysis, RNA
chemical_list: D017931:DNA Primers; D015345:Oligonucleotide Probes; D012335:RNA, Ribosomal