University of Vienna   
Department of Microbial Ecology
   
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when probeBase has been updated!
probeBase comprises currently 2788 probes, 175 primer, 16 microarrays, and 499 references.

 
 
 
 
 
 
 

Evaluation of primer pairs using probeBase and SILVA TestPrime
Direct submission of primer sequences from probeBase to the  SILVA TestPrime tool facilitates evaluation of specificity and coverage of primer combinations.  Test with primer 27f
Primers for diversity surveys
probeBase now also contains more than 150 published PCR primers targeting the 16S/18S rRNA genes of Bacteria, Archaea, and Eukaryotes. For each primer the coverage of the three domains is included (based on the  SILVA SSU Ref 108 NR dataset). Frank Oliver Glöckner, Anna Klindworth and the SILVA team are greatly acknowledged for contribution of primer details and calculation of coverage values.  List of primer sequence at probeBase
A detailed description of the evaluation of these primers is available in: Klindworth A, Pruesse E, Peplies J, Quast C, Horn M, Glöckner FO. 2012. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next generation sequencing based diversity studies. Nucleic Acids Res. 10.1093/nar/gks808  Full text
 
probeCheck
probecheck is a 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

Recently added to probeBase
Probes
 help-volv2
(Rickettsial endosymbionts of Carteria, Pleodorina, Volvox (green algae) and Diophrys appendiculata (ciliate))
 help-volv1
(Rickettsiaceae)
 volv-835
(Rickettsial endosymbionts hosted by Carteria, Pleodorina, Volvox (green algae) and Diophrys appendiculata (ciliate))
Papers
Kawafune K, Hongoh Y, Hamaji T, Nozaki H. 2012. Molecular Identification of Rickettsial Endosymbionts in the Non-Phagotrophic Volvocalean Green Algae. PLoS ONE 7(2): e31749. doi:10.1371/journal.pone.0031749
Zimmermann J, Lott C, Weber M, Ramette A, Bright M, Dubilier N, Petersen JM. Co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent (unpublished)
Johnson K, Jiang Y, Kleerebezem R, Muyzer G and Van Loosdrecht MCM. 2009. Enrichment of a Mixed Bacterial Culture with a High Polyhydroxyalkanoate Storage Capacity. Biomacromolecules 2009 10 (4), 670-676

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

probeBase update history
• link to TestPrime included (30.07.12)
• general primers added, minor layout changes (16.07.12)
• 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.  Full text
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