by A. Loy, F. Maixner, M. Wagner, M. Horn
probeBase is maintained by the Department of Microbial Ecology at the University of Vienna. Please help to ensure that probeBase remains an up-to-date resource for oligonucleotide probe sequences by submitting missing or new probes!
References: If you use probeBase as a tool in your published research, we ask that either of these papers be cited:
Suggested wording: (i) "Oligonucleotide probe sequences have been deposited at probeBase.", or (ii) "Details on oligonucleotide probes are available at probeBase."
- 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
- Loy, A., Horn, M., Wagner, M. 2003. probeBase - an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31: 514-516.
Acknowledgement: Frank Oliver Glöckner, Anna Klindworth and the SILVA team are greatly acknowledged for contribution of primer details and calculation of coverage values. We are indebted to Safak Yilmaz and Daniel Noguera for calculation of the ΔG values. We greatly thank Todd DeSantis for his efforts to facilitate the access to Green Genes and acknowledge help of Christian Baranyi for statistical analysis and of Carmen Krammer, Manuela Hartmann, and Silvia Weber for database maintenance. We further thank Phil Hugenholtz for valuable comments and all users who contributed to probeBase by submitting probes.
ΔG values were calculated according to Yilmaz and Noguera (2006). Making all Parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl Environ Microbiol 72: 733-744. Abstract.
probeBase offers direct submission of sequences to probeCheck at the Department of Microbial Ecology (University of Vienna).
probeBase offers direct submission of sequences to the TestProbe and TestPrime tools of SILVA at the Max Planck Institute for Marine Microbiology.
probeBase offers direct submission of sequences to the probe match tool of the Ribosomal Database Project II at the Center for Microbial Ecology (Michigan State University).
probeBase offers direct submission of sequences to the simrank tool of Green Genes at the Lawrence Berkeley National Laboratory.
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