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Graphical representation of ribosomal RNA probe accessibility data using ARB software package

Yadhu Kumar1, Ralf Westram1, Sebastian Behrens2, Bernhard Fuchs2, Frank Oliver Glöckner23, Rudolf Amann2, Harald Meier4 and Wolfgang Ludwig1*

Author Affiliations

1 Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising Germany

2 Max Plank Institute for Marine Microbiology, D-28359 Bremen, Germany

3 International University Bremen, D-28759 Bremen, Germany

4 Lehrstuhl für Rechnertechnik und Rechnerorganisation, Technische Universität München, D-85748 Garching, Germany

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BMC Bioinformatics 2005, 6:61  doi:10.1186/1471-2105-6-61

Published: 21 March 2005

Abstract

Background

Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments.

Results

The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool.

Conclusion

Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de webcite.