title: Graphical representation of ribosomal RNA probe accessibility data using ARB software package.
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.
  
  
  CONCLUSIONS
  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
authors.affiliation: Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany. yadhu@mikro.biologie.tu-muenchen.de
authors.forename: Yadhu
authors.initials: Y
authors.lastname: Kumar
authors.forename: Ralf
authors.initials: R
authors.lastname: Westram
authors.forename: Sebastian
authors.initials: S
authors.lastname: Behrens
authors.forename: Bernhard
authors.initials: B
authors.lastname: Fuchs
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
authors.forename: Rudolf
authors.initials: R
authors.lastname: Amann
authors.forename: Harald
authors.initials: H
authors.lastname: Meier
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Ludwig
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics*; D003196:Computer Graphics; D003198:Computer Simulation; D017931:DNA Primers; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D005798:Genes, Bacterial / Q000235:genetics*; D017403:In Situ Hybridization; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020407:Internet; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry*; D010802:Phylogeny; D011381:Programming Languages; D012313:RNA; D015347:RNA Probes / Q000737:chemistry; D012329:RNA, Bacterial; D012335:RNA, Ribosomal / Q000032:analysis* / Q000737:chemistry; D012270:Ribosomes; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D015345:Oligonucleotide Probes; D015347:RNA Probes; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012313:RNA