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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 2568 probes, 16 microarrays, and 352 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
18Alf-1437
(Methanotrophic symbiont of Sphagnum mosses) | 18Alf-0218
(Methanotrophic symbiont of Sphagnum mosses) | MIN1586
(Mycobacterium intracellulare) | MIN351
(Mycobacterium intracellulare) | MAC2543
(Mycobacterium avium complex) |
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Most recent papers
| Raghoebarsing AA, Smolders AJ, Schmid MC, Rijpstra WI, Wolters-Arts M, Derksen J, Jetten MS, Schouten S, Sinninghe Damste JS, Lamers LP, Roelofs JG, Op den Camp HJ, Strous M. 2005. Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436: 1153-6 | | St. Amand AL, Frank DN, De Groote MA, Pace NR. 2005. Use of Specific rRNA Oligonucleotide Probes for Microscopic Detection of Mycobacterium avium Complex Organisms in Tissue. J. Clin. Microbiol. 43: 1505–1514 | | St. Amand AL, Frank DN, De Groote MA, Basaraba RJ, Orme IM, Pace NR. 2005. Use of Specific rRNA Oligonucleotide Probes for Microscopic Detection of Mycobacterium tuberculosis in Culture and Tissue Specimens. J. Clin. Microbiol. 43: 5369-5371 |
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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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