Related Experiment Videos
probeBase: an online resource for rRNA-targeted oligonucleotide probes
Alexander Loy1, Matthias Horn, Michael Wagner
1Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany.
Nucleic Acids Research
|January 10, 2003
Summary
ProbeBase is a database of over 700 ribosomal RNA-targeted oligonucleotide probes for identifying microorganisms. It aids researchers in finding suitable probes for environmental and clinical samples.
Area of Science:
- Microbiology
- Bioinformatics
- Molecular Biology
Background:
- Ribosomal RNA (rRNA)-targeted oligonucleotide probes are essential for culture-independent microbial identification in various sample types.
- A centralized, accessible resource for these probes is crucial for researchers.
Purpose of the Study:
- To introduce ProbeBase, a comprehensive online database of published rRNA-targeted oligonucleotide probes.
- To provide researchers with a tool for identifying suitable probes and aiding in the development of new ones.
Main Methods:
- Compilation of over 700 published rRNA-targeted oligonucleotide probe sequences with bibliographic and biological annotations.
- Integration of probe match tools from ARB software and Ribosomal Database Project II (RDP-II) for specificity analysis.
- Development of search functionalities including 'search probeBase', 'find probe set', and 'search target site'.
Main Results:
- ProbeBase offers detailed information including target organisms, rRNA targets, G+C content, melting temperature, and references.
- Probes validated for fluorescence in situ hybridization (FISH) are highlighted with recommended conditions.
- The database facilitates probe selection and supports the design of novel FISH probes.
Conclusions:
- ProbeBase serves as a valuable resource for researchers in microbiology and related fields.
- The database enhances the efficiency of identifying microorganisms and developing new molecular probes.