ArticleBMC bioinformatics2005
Graphical representation of ribosomal RNA probe accessibility data using ARB software package.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Molecular Detection of the Harmful RaphidophyteTropical life sciences research · 2023Article
- Molecular Techniques for the Detection of Organisms in Aquatic Environments, with Emphasis on Harmful Algal Bloom Species.Sensors (Basel, Switzerland) · 2017Review
- Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties.Cell host & microbe · 2016Article
- Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.RNA (New York, N.Y.) · 2015Article
- Specific detection and localization of microsporidian parasites in invertebrate hosts by using in situ hybridization.Applied and environmental microbiology · 2013Article
- mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.Applied and environmental microbiology · 2011Article
- Molecular systematics and ultrastructural characterization of a forgotten species: Chattonidium setense (Ciliophora, Heterotrichea).Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2006Article
- Molecular biological detection of anaerobic gut fungi (Neocallimastigales) from landfill sites.Applied and environmental microbiology · 2006Article
- Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.BMC bioinformatics · 2006Article
- Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides.Applied and environmental microbiology · 2006Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTaxon 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.
resultsThe 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.
conclusionUsing 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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