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.
Highlights
Our understanding of the diversity and role of microorganisms on our planet is to a great extent based on exploiting the ribosomal RNA as phylogenetic marker molecule in diagnostic molecular biology and microscopy assays
While rRNA-targeted oligonucleotides have been applied in different sorts of diagnostic formats such as DNA microarrays (PhyloChips) [1,2] and denaturing gradient gel electrophoresis [3], they are most widely used for amplicon sequencing and fluorescence in situ hybridization (FISH) [4]
Highly multiplexed amplicon sequencing with rRNA-targeted primers enables surveying microbial diversity across numerous samples [5,6], which provides unprecedented insights into the spatial distribution and temporal dynamics of the diverse microbial communities that thrive in the environment [7] or are associated with eukaryotic hosts [8,9]
Summary
Our understanding of the diversity and role of microorganisms on our planet is to a great extent based on exploiting the ribosomal RNA as phylogenetic marker molecule in diagnostic molecular biology and microscopy assays. ProbeBase was originally established in 2002 [14] to provide a common, freely accessible repository for rRNA-targeted oligonucleotide sequences, including contextual information and multiple options for testing in silico specificity and coverage [15] against up-to-date rRNA sequence databases such as RDP-II [16] and SILVA [17]. Finding appropriate oligonucleotides with a suite of ‘Search’ and sequence ‘Match’ tools provides convenient access to the information in the database.
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