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probeBase newsletter
Get a list of all new probes
when probeBase has been updated!
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probeBase comprises currently 2538 probes, 16 microarrays, and 341 references. |
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Search
Search probeBase for target organisms, probe names, accession numbers, microarrays, target site, references.
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Match
Match your 16S rRNA sequence(s) against probeBase and find all published probes targeting your sequence(s).
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Lists
View lists of probes (according to probe categories), coverage of group-specific probes, microarrays, references, etc.
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Submission
Submit new or missing probes to probeBase.
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FAQ
Frequently Asked Questions
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Links
Websites relevant to ribosomal RNA
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Credits
Credits and acknowledgements
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 probeCheck
We have recently set up probecheck, a new web server for convenient testing of probe and primer specificity and coverage. probeCheck uses an extendable list of established sequence databases including the rRNA databases Silva, RDP-II, and Greengenes, and the functional gene databases of FGPR. probeCheck webserver
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Most recent probes
Aqs997
(Microcolonies of a dominant denitrifying bacterium in activated sludge, closely related to bacteria in the Aquaspirillum genus in the Neisseriaceae family) | UP23b
(Urothoe poseidonis clone UP23b) | Modesto
(Modestobacter genus) | Geo/Blasto
(Geodermatophilus/Blastococcus group) | YERU
(Yersinia ruckeri type I) |
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Most recent papers
| Thomsen TR, Nielsen JL, Ramsing NB, Nielsen PH. 2004. Micromanipulation and further identification of FISH-labelled microcolonies of a dominant denitrifying bacterium in activated sludge. Environ Microbiol 6: 470-9 | | Gillan DC, Dubilier N. 2004. Novel epibiotic thiothrix bacterium on a marine amphipod. Appl Environ Microbiol 70: 3772-5 | | Urzi C, La Cono V, Stackebrandt E. 2004. Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH). Environ Microbiol 6: 678-85 |
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Contribute to probeBase!
The value of probeBase depends upon your help.
Publish your oligonucleotide sequence in probeBase! |
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probeBase update history
| • | link to probeCheck included (14.09.07) |
| • | direct submission of probe sequences to the simrank tool at Greengenes implemented (06.09.06) |
| • | list of coverage of group-specific probes updated and newly implemented (30.08.06) |
| • | search for microarray probes, probe sequences implemented (15.08.06) |
| • | print view added for probe details, FAQ added (01.08.06) |
| • | freely editable user comments for each probe (29.07.05) |
| • | new search interface and options, major layout changes (29.07.05) |
| • | unique probeBase accession numbers added for all probes (28.07.05) |
| • | delta G values (Yilmaz et al., 2004) included for all probes (28.07.05) |
| • | user statistics available (17.01.05) |
| • | search for references implemented (19.11.04) |
| • | search target site functions returns consensus brightness classes according to Behrens et al. (19.11.04) |
| • | newsletter and sidebar added (17.11.04) |
| • | possibility to submit probes prior to publication (by hiding the nucleotide sequence) implemented (14.11.04) |
| • | new RDP-II probe match tool implemented (07.09.04) |
| • | search probebase by categories implemented (11.02.03) |
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If you use probeBase as a tool in your published research, we ask that this paper be cited:
Loy A, Maixner F, Wagner M, Horn M. 2007. probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res. 35: D800-D804. PDF
Suggested wording: (i) "Oligonucleotide probe sequences have been deposited at probeBase.", or (ii) "Details on oligonucleotide probes are available at probeBase."
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