There has been a lot of discussion recently about which region(s) of bacterial 16S rRNA are the best (most informative, easily amplified, and short) for phylogenetic inference, particularly when using Illumina reads (e.g. Schloss 2010 PMID 20628621).
I have two different pictures in my head when thinking about the 16S rRNA sequence, the linear one of the sequence, and the two-dimensional one of secondary structure. I thought it might be useful to map the secondary structure onto the primary sequence. I've used the E. coli rrnB gene sequence as the reference. Error-correction is welcome.
The colors have no special meaning except that blue and red were chosen for short-range interactions.
The authoritative reference seems to be Neefs 1990 PMID 1692117. Here is a birds-eye-view. The secondary structure shown in these figures is from Case et al 2007 PMID 17071787.
I found a nice introductory post about the topic (here).
