Ribosome binding model using a codebook and exponential metric

A model based on a variable length codebook and a metric is used to model the process of translation in gene expression. In this model it is assumed the ribosome decodes the mRNA sequence by using the 3´end of the 16SrRNA molecule as an embedded codebook. The metric uses an exponential algorithm to recognize the Shine Dalgarno (SD) sequence that allows detecting this sequence in each gene without the averaging used by Dawy et al. (2005). The E.Coli 0157:H7 Sakai sequence data is used in this model and the validity of the results is proved by the ability of detecting the Shine Dalgarno in translation. The initiation codon still can be found by averaging using the method used by Dawy et al. (2005). Mutations are also studied for Jacob, Hui and De Boer cases. Results are compared to biological data and prove to be consistent.