The rpos/rprec30 method of Charneski and Hurst. (A) As a measure of the stalling effect of a codon (or group of codons beginning) at position 0, the occupancy of all codon positions (rpos) from 30 codons upstream (position −30) to 30 codons downstream (position 30) of the putative stalling codon was divided by the mean occupancy of upstream codons −30 to −1 (rprec30, indicated by the bracket). (B) This produced a normalized pausing value (rpos/rprec30), where a value of one represents the average rate of translation. (C) After averaging the rpos/rprec30 values among all similar groups of codons, the AUC (indicated by the shaded purple area) of the mean-normalized occupancy values from position 0 until the position where mean occupancy returned to the average was used as a measure of the stalling effect (if positive).
