Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package |
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| Authors: | Yadhu Kumar Ralf Westram Peter Kipfer Harald Meier and Wolfgang Ludwig |
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| Institution: | (1) Lehrstuhl fr Mikrobiologie, Technische Universitt Mnchen, D-85350 Freising, Germany;(2) Lehrstuhl fr Computer Graphik und Visualisierung, Technische Universitt Mnchen, D-85748 Garching, Germany;(3) Lehrstuhl fr Rechnertechnik und Rechnerorganisation, Technische Universitt Mnchen, D-85748 Garching, Germany |
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| Abstract: | 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 three-dimensional 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. |
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