Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using

Background: Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with threedimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results: Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the disp...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Yadhu Kumar, Ralf Westram, Peter Kipfer, Harald Meier, Wolfgang Ludwig
• Keywords: BMCBI 2006, RRNA, Sequence Alignments, Three-dimensional Structure