The Genomic Pattern of tDNA Operon Expression in E. coli
Figure 3
Effect of Clustering Radius on the Number of tDNA Clusters Obtained in the E. coli K12 Genome (Calculated in Steps of 25 bp)
Clustering radius (r) is the maximum distance from one end of a tDNA in bp within which part of another co-linear tDNA must fall to be joined into the same cluster. Vertical dashed line shows the value used in this study (r = 300 bp), which correctly recovered all but three of the 44 experimentally known tDNA operons (indicated by horizontal dashed line). These three, ribosomal operons all, were not correctly recovered until a much higher radius was used but then within only a narrow range (2,400 ≤ r ≤ 2,800 bp) before a false positive was encountered. Thus, the natural proximity of tDNAs within operons made it possible through tDNA coordinates and strandedness alone to recover most of the true operons in E. coli K12.