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Updated: Jul 10, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
A computational model for reading frame maintenance
L Ponnala1, D L Bitzer, A Stomp
1Dept. of Electr. & Comput. Eng., North Carolina State Univ., Raleigh, NC 27695, USA.
Abstract:
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship between cumulative signal phase and reading frame. Based on this observation, we have developed a model that indicates how likely it is for the ribosome to stay in frame throughout the process of elongation. We validate this model by analyzing verified coding sequences in E. coli.
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