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. 2014 Dec;24(12):2011–2021. doi: 10.1101/gr.175893.114

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© 2014 Artieri and Fraser; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 5. — The r_pos/r_prec30 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 (r_pos) 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 (r_prec30, indicated by the bracket). (B) This produced a normalized pausing value (r_pos/r_prec30), where a value of one represents the average rate of translation. (C) After averaging the r_pos/r_prec30 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).