%0 Journal Article
%T Graphical representation of ribosomal RNA probe accessibility data using ARB software package
%A Yadhu Kumar
%A Ralf Westram
%A Sebastian Behrens
%A Bernhard Fuchs
%A Frank Gl£¿ckner
%A Rudolf Amann
%A Harald Meier
%A Wolfgang Ludwig
%J BMC Bioinformatics
%D 2005
%I BioMed Central
%R 10.1186/1471-2105-6-61
%X 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.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.The introduction and use of comparative sequence analysis of appropriate marker genes as a powerful tool in taxonomy has substantially contributed to the rapid growth of molecular sequence databases such as EMBL [1], GenBank [2], and ribosomal RNA (rRNA) databases [3-5]. Evidently, molecular phylogenetic analyses have greatly influenced the restructuring of systematics especially in the case of prokaryotes. Nowadays, identification and classification at the species and higher taxonomic levels mainly relies on a genotypic approach, typically involving an analysis of small, and to a lesser extent, large ribosomal RNA gene (rRNA) structures. The backbone of the current taxonomy of the prokaryotes is almost exclusively based upon a phylogenetic network derived from comparative sequence analysis of the small subunit rRNAs and respective phylogenetic marker genes [6]. As 'living fossil
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