An Optimized Ribosome Binding Model Using Communication Theory Concepts

Regulatory elements in genetic data are often short and variable, their identification and discovery using computational algorithms is difficult. A model based on communication theory concepts and used by Dawy, et al., [1], is used to model the process of translation in gene expression. The model assumes the ribosome decodes the mRNA sequence by using the 3’ end of the 16SrRNA molecule as an embedded codebook. In this work we used an optimized algorithm to obtain the Shine-Dalgarno (SD) sequence that allows detecting this sequence in the genes without the averaging used in [1]. The validity of the model is established by the ability of detecting the Shine-Dalgarno in translation, the initiation codon still can be obtained by averaging as in [1]. Mutations are also studied for De Boer case. Results are compared to biological data and proved to be consistent.