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

Kumar, Y., Westram, R., Behrens, S., Fuchs, B., Glockner, F. O., Amann, R., et al. (2005). Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics, 6: 61.

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Behrens5.pdf (Verlagsversion), 9MB
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Kumar, Y., Autor
Westram, R., Autor
Behrens, S.1, Autor           
Fuchs, B.1, Autor           
Glockner, F. O.2, Autor           
Amann, R.1, Autor           
Meier, H., Autor
Ludwig, W., Autor
Affiliations:
1Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481696              
2Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481697              

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 Zusammenfassung: 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.

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Sprache(n): eng - English
 Datum: 2005-03-21
 Publikationsstatus: Erschienen
 Seiten: 9
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: eDoc: 250523
ISI: 000228380800001
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Titel: BMC Bioinformatics
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: BioMed Central
Seiten: - Band / Heft: 6 Artikelnummer: 61 Start- / Endseite: - Identifikator: ISSN: 1471-2105
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905000