Go to the abstract in the NAR 2003 Database Issue.
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Lehrstuhl fuer Mikrobiologie Technische Universitaet Muenchen D-85350 Freising Germany
Contact horn@microbial-ecology.de
Ribosomal RNA-(rRNA)-targeted oligonucleotide probes are widely used for culture-independent identification of microorganisms in environmental and clinical samples. ProbeBase is a comprehensive database containing more than 700 published rRNA-targeted oligonucleotide probe sequences (status August 2002) with supporting bibliographic and biological annotation that can be accessed through the internet at http://www.probebase.net. Each oligonucleotide probe entry contains information on target organisms, target molecule (small- or large-subunit rRNA) and position, G+C content, predicted melting temperature, molecular weight, necessity of competitor probes, and the reference that originally described the oligonucleotide probe, including a link to the respective abstract at PubMed. In addition, probes successfully used for fluorescence in situ hybridization (FISH) are highlighted and the recommended hybridization conditions are listed. ProbeBase also offers difference alignments for 16S rRNA-targeted probes by using the probe match tool of the ARB software and the latest small-subunit rRNA ARB database (release June 2002). The possibility to directly submit probe sequences to the probe match tool of the Ribosomal Database Project II (RDP-II) further allows to extract supplementary information on probe specificities. The two main features of probeBase, 'search probeBase' and 'find probe set', help researchers to find suitable, published oligonucleotide probes for microorganisms of interest or for rRNA gene sequences submitted by the user. Furthermore, the 'search target site' option provides guidance for the development of new FISH probes.
We gratefully acknowledge Wolfgang Ludwig for providing the ARB software and the ARB database to the scientific community. We thank James R. Cole from RDP-II for his support, Manuela Hartmann and Silvia Weber for their help with database administration, and Klaus Ungerer for his generosity.
Loy, A., Horn, M., Wagner, M. 2002. probeBase - an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res., in press.
Category Varied Biomedical Content
Go to the abstract in the NAR 2003 Database Issue.