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Get a list of all new probes
when probeBase has been updated!
probeBase comprises currently 1469 probes, 9 microarrays, and 295 references.

 
 
 
 
 
 
 

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
 Bnix-1249
("Candidatus Endonucleobacter bathymodioli")
 Bnix-643
("Candidatus Endonucleobacter bathymodioli")
 Bnix-64
("Candidatus Endonucleobacter bathymodioli")
 BKH132
(uncultured eubacterium WD2116 (AJ292648), uncultured eubacterium WD2114 (AJ292647), L19-K36)
 BKH131
(Uncultured bacterium clone 015B-A07 (AY662004), uncultured beta proteobacterium Elb271 (AJ421941), M3-K7)
Most recent papers
'Zielinski, F. U., A. Pernthaler, S. Duperron, L. Raggi, O. Giere, C. Borowski, and N. Dubilier. (in prep.) Widespread Occurrence of an Intranuclear Bacterial Parasite in Vent and Seep Mussels.
Nelson, B.P., Liles, M.R., Frederick, K.B., Corn, R.M., and Goodman, R.M. (2002) Label-free detection of 16S ribosomal RNA hybridization on reusable DNA arrays using surface plasmon resonance imaging. Environ Microbiol 4: 735-743.
Sanguin, H., Herrera, A., Oger-Desfeux, C., Dechesne, A., Simonet, P., Navarro, E., et al. (2005) Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol 8: 289-307.

Contribute to probeBase!
The value of probeBase depends upon your help.
Publish your oligonucleotide sequence in probeBase!

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)
 View probeBase user statistics

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."
by Alexander Loy, Frank Maixner, Michael Wagner, Matthias Horn
 Acknowledgment
Questions, comments, bug reports, and suggestions are welcome at
 probebase@microbial-ecology.net