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Last update on 25. Nov 2018 .
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Visualization of Three-dimensional structure of small subunit (16S) rRNA

OCCURRENCE

In Primary Sequence Editor (ARB_EDIT4)

 

DESCRIPTION

This program (RNA3D) displays the three-dimensional structure of small subunit (16S) rRNA in OpenGL 3D environment. The annotation of RNA three-dimensional structures consists of a preprocessing of the information embedded in their 3D coordinates. It processes PDB structural information stored in the PDB file (1M5G) and used for further structural analysis and searches. To provide user with the more detailed perspective of 16S rRNA structure, structural information corresponding to the ribosomal proteins were excluded during processing. The extracted structural information is then fed to OpenGL engine, where it is further transformed into a hierarchy of OpenGL objects, which encode molecule chains, residues and base positions. At this stage, further processing may occur, for example when the user requests the mapping of secondary structure information of rRNA onto the molecule in the form of loops and stems. Any information derived from the multiple alignments (phylogenetic information) is merged into the structural information or rRNA molecule in the post-processing step.

 

NOTES

More information regarding merging secondary structure information and mapping individual rRNA sequence,sequence associated data, oligo-nucleotide probes can be found in the respective help files. See "Subtopics" section.

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known