Figure 1. A
representation of hypervariable regions within the 16S rRNA gene.
The
plotted line reflects fluctuations in variability amongst aligned 16S
rRNA gene sequences; peaks reflect greater conservation, whilst troughs
correspond to the known hypervariable regions V1 to V9 indicated by the
red bars.
The figure was generated as follows:
the frequency of the most common
nucleotide residue was calculated for each base position within an
alignment of 4,383 sequences from Bacteria type strains. The
resulting frequency distribution F was
then smoothed, by taking the mean frequency within a 50 base sliding
window moving 1 base position at a time along the alignment. For
further details on calculating F click here.
Note that frequency distribution F is the reverse of probability
distribution Q used to calculate expected percentage
difference values as used by the Pintail
algorithm.
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