Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs
Fig 1
Percentage of species with depleted SD-like sequences.
The “Diwan Dataset” comprises the 284 prokaryotes studied by Diwan et al., but filtered for the subset (222) that demonstrably contains a perfect antiSD (CCUCCU) in the tail of the 16S rRNA (Amin et al., submitted). The “Control Dataset” comprises the 128 prokaryotes that lack a CCUCCU antiSD (Amin et al., submitted). The “Diwan high affinity codon shuffle” is the method used by Diwan et al. 2016 [8], and which uses high-affinity hexamers to define SD-like motifs. The “Complementary codon shuffle” is the method used here, using hexamers that are a 5-of-6 match to AGGAGG. The “Combined P-val” is the combination of the complementary codon shuffle with the codon usage metric. Depletion is scored at a p-value of 0.05. Results were not FDR corrected, because the distribution of p-values was not uniform.