probeBase

• University of Vienna, Department of Microbiology and Ecosystem Science

probeBase 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.
The major features of probeBase include a classification of probes and primers according to the NCBI taxonomy database, a powerful and customizable search function, which serves to query for target organisms, probe names, primers, target sites, and references. The probeBase match tool can be used to match near-full length rRNA sequences against probeBase and find all published probes targeting the query sequences. The new proxy match tool extends this analysis to partial rRNA sequences, which exploits full-length sequences in the rRNA sequence database SILVA to find published probes potentially targeting partial query sequences. A tool for submitting new or missing probe sequences or references helps to keep probeBase up-to-date.