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Last update on 08. Apr 2009 .
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Superimposing rRNA sequence data, SAI and probes

OCCURRENCE

In ARB primary structure editor (ARB_EDIT4) -> RNA3D

 

DESCRIPTION

SUPERIMPOSING rRNA SEQUENCE DATA Any rRNA sequence contained in the multiple sequence alignments of ARB primary structure editor can be overlaid onto the structure of E. coli in the RNA3D window. Desired rRNA sequence to be mapped onto the structure can be selected by the left mouse button in the multiple sequence alignment and the selected rRNA sequence will be instantly mapped onto the master structure.

The selected rRNA sequence is annotated with mutation (base substitutions), insertion and deletion information at each site as compared to the master sequence (E. coli).

For the regions where the sequences are aligned without deletion or insertion, direct base substitution (mutation) is applied. Because the C’---C’ distance is essentially the same (~10.2 Å) in all Watson-Crick base pairs (Watson and Crick, 1953), this simple procedure preserves the base pairing and the double helical structure while substituting the bases. Although there do exist the requirement of structural adjustments for non-Watson-Crick base pairs, currently, simple base substitut