University of Vienna   
Department of Microbial Ecology
There is a new probeBase version! Please follow this link to experience the new probeBase.

Ribosomal RNA (rRNA) targeted oligonucleotide probes are widely used for fluorescence in situ, dot blot, and microarray hybridization in culture-independent studies of microbial communities and for the identification of uncultured prokaryotes in clincal and environmental samples. probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information.
probeBase can be searched for target organisms, probe names, probe sequences, probe accession numbers, and references. The "search target site" function can assist in the development of new rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH).
The "match" tool can be used to rapidly retrieve all published probes targeting your query sequences (e.g. from a rRNA gene clone library) without prior phylogenetic analysis. probeBase is hyperlinked with PubMed, RDP-II, and Greengenes to provide additional bibliographic information and up-to-date data on probe specificity.
probeBase is described in: Loy, A., Horn, M., Wagner, M. (2003) probeBase - an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31, 514-516.  PDF
What orientation has the probe sequence in probeBase?
Most probe sequences in probeBase are in antisense orientation (i.e. they can be applied to directly detect ribosomal RNA in, for example, fluorescence in situ hybridization experiments). In order to avoid errors, users should always carefully check the orientation of a probe sequence prior to application.
I have a (collection of) rRNA sequence(s) and want to find suitable perfectly-matching probes?
Using the "Find probe set" tool of probeBase it is possible to simultaneously match up to 150 rRNA (gene) sequences (FastA format) with all probes in the database and to find all probes perfectly-matching the query sequences.
Can I design new probes with probeBase?
No. ProbeBase contains already available rRNA-targeted oligonucleotide probes plus associated information and offers tools to assess functionality and up-to-date specificity of these probes.
I am looking for an already published probe but I can not find it at probeBase?
We are trying to implement all already published probes in probeBase but some probes might have been overlooked. In order to keep probeBase as up-to-date as possible, we ask you to submit the missing probe or probe information to probebase via our online submission form.
Can I edit the annotation of my probes after they have been posted on the probeBase webpage?
Not directly via the probeBase webpage, but you can send an email indicating the desired changes to The updated information will appear on the website upon the next regular update of probeBase.
Can I purchase oligonucleotide probes via probeBase?
No. ProbeBase is a freely-accessible, non-commercial database for rRNA-targeted oligonucleotide probes maintained by the Department of Microbial Ecology, University of Vienna, Austria. To buy probes we ask you to contact a commercial oligonucleotide supplier.
I can not access probeBase via the link!
ProbeBase is currently not available at but can be accessed via our department's homepage at
by Alexander Loy, Frank Maixner, Michael Wagner, Matthias Horn
Questions, comments, bug reports, and suggestions are welcome at