%0 Journal Article
%T Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package
%A Yadhu Kumar
%A Ralf Westram
%A Peter Kipfer
%A Harald Meier
%A Wolfgang Ludwig
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-240
%X Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA.Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de webcite.The backbone of the modern taxonomy of the prokaryotes is almost exclusively based upon a phylogenetic network derived from comparative sequence analysis of the small subunit ribosomal RNA (rRNA) and the respective phylogenetic marker genes [1]. Since the function of rRNA is largely determined by its structure [2] and the general structure of rRNA is universally conserved across all the taxa that have been examined [3,4], the structural features of rRNA, even when not universally identical across the taxa, is more highly conserved than are t
%U http://www.biomedcentral.com/1471-2105/7/240