probeBase—an online resource for rRNA-targeted oligonucleotide probes: new features 2007

By A. Loy, F. Maixner, Michael Wagner, M. Horn. Nucleic Acids Res., 2006

532 citations recorded by the source corpus.

probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at . Email correspondence can be addressed to probebase@microbial-ecology.net.

Subfields: Ecology, Molecular Biology, Pollution

View Paper: https://www.semanticscholar.org/paper/b954bfc46f4e72865a50ee8f8b8681606459edfe

How researchers see this paper

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In Ecology

1. G. Berg
2. Bernhard Fuchs
3. R. Koga
4. Jörg Peplies
5. R. Amann
6. Elmar Pruesse
7. Jeffrey I. Gordon
8. W. Kwong

In Molecular Biology

1. W. Garrett
2. Rob Knight
3. Frank Oliver Glöckner
4. Jörg Peplies
5. Christian Quast
6. Laurie H. Glimcher
7. N. Moran
8. Philipp Engel

In Pollution

1. G. Berg
2. R. Amann
3. Bernhard Fuchs
4. W. Garrett
5. B. Lugtenberg
6. Martin Grube

Citations in the corpus

• Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques (2008, background): “net/probebase/">probeBase (see Further information) team in Vienn”
• The SILVA ribosomal RNA gene database project: improved data processing and web-based tools (2012, background): “Both TestProbe and TestPrime are cross-linked with the oligonucleotide signature database probeBase (23).”
• Standard methods for research on Apis mellifera gut symbionts (2013, methodology): “When proportional abundance is used, a and b equal 1 and the index collapses to 1-w. b. UniFrac distances (Lozupone and Knight, 2005).”
• Bacterial Endophytes: Who and Where, and What are they doing there? (2013, background): “Naturally occurring endophytes can be visualized by FISH (fluorescence in situ hybridization) combined with confocal laser scanning microscopy using specific probes (Amann et al. 1990; Loy et al. 2007).”
• Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis (2010, methodology): “The sequences of the following FISH probes were obtained from probeBase (http://www.microbial-ecology. net/probebase/) (Loy et al., 2007): the ‘‘universal’’ bacterial probe-EUB338 (pB-00159), Enterobacteriaceae targeted probe (pB-00914), K. pneumoniaedirected probe (pB-00352), and P. mirabilis…”