BIOINFORMATICS Vol. 00 no. 00 Pages 18 A model for +1 frameshifts in eubacteria

Motivation: This work applies the methods of signal processing and the concepts of control system design to model the maintenance and modulation of reading frame in the process of protein synthesis. The model shows how translational speed can modulate translational accuracy to accomplish programmed +1 frameshifts and could have implications for the regulation of translational efciency. Results: A series of free energy estimates were calculated from the ribosome's interaction with mRNA sequences during the process of translation elongation in eubacteria. A sinusoidal pattern of roughly constant phase was detected in these free energy signals. Signal phase was identied as a useful parameter for locating programmed +1 frameshifts encoded in bacterial genes for release factor 2. A displacement model was developed that captures the mechanism of frameshift based on the information content of the signal parameters and the relative abundance of tRNA in the bacterial cell. Results are presented using experimentally veried frameshift genes across eubacteria. Availability: A set of MATLAB ® programs that implement our methods are available upon request from the corresponding author. Contact