 | |
probeBase newsletter
Get a list of all new probes
when probeBase has been updated!
|
|
probeBase comprises currently 2620 probes, 16 microarrays, and 373 references. |
 |
Search
Search probeBase for target organisms, probe names, accession numbers, microarrays, target site, references.
|
| |
Match
Match your 16S rRNA sequence(s) against probeBase and find all published probes targeting your sequence(s).
|
| |
Lists
View lists of probes (according to probe categories), coverage of group-specific probes, microarrays, references, etc.
|
| |
Submission
Submit new or missing probes to probeBase.
|
| |
FAQ
Frequently Asked Questions
|
| |
Links
Websites relevant to ribosomal RNA
|
| |
Credits
Credits and acknowledgements
|
 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
|
Most recent probes
Dbact653
(Desulfococcus/Desulfosarcina/Desulfonema) | Proti_467
(primary symbiont of Euplotes samples POH1, EM, FL(12)-VI) | Proti_445
(primary symbiont of Euplotes samples POH1, EM, FL(12)-VI) | Lepto175
(Leptothrix ochracea) | RHIZ1244
(Order Rhizobiales) |
|
Most recent papers
| Nielsen JL and Hansen AA. 2009 Identification of denitrifying microorganisms in activated sludge by FISH. In: FISH handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH (Nielsen, P., Daims, H. Lemmer, H. ed) IWA Publishing, London, UK, p. 19-24. | | Miyatake T, MacGregor BJ and Boschker HTS. 2009. Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA. Appl. Environ. Microbiol. 75: 4927-4935. | | Vannini C, Ferrantini F, Verni F, Ristori A and Petroni G. Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association. Unpublished. |
|
Contribute to probeBase!
The value of probeBase depends upon your help.
Publish your oligonucleotide sequence in probeBase! |
 |
probeBase update history
| • | link to TestProbe included (19.01.12) |
| • | 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) |
|
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."
|
|
|
