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probeBase


NAR Molecular Biology Database Collection entry number 390
Loy A., Maixner, F, Wagner M. and Horn M.
Department of Microbial Ecology, University of Vienna, A-1090 Vienna, Austria

Database Description

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 1,200 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.

Acknowledgements

The authors 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 Greengenes 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.

References

1. Loy, A., Maixner, F., Wagner, M., Horn, M. 2007. probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res., in press.
2. Loy, A., Horn, M., Wagner, M. 2003. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res., 31, 514-516.


Go to the abstract in the NAR 2007 Database Issue.
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