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

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 patt...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier, Wolfgang Ludwig
• Keywords: ARB Software Package, BMCBI 2005, Oligonucleotide Probes, Probe Accessibility Data