An augmented block code model for protein translation using free energy based distance decoders

Informational analysis of genetic sequences has revealed the existence of significant analogies between the genetic process and information processing systems used in the field of communications engineering. By analyzing key elements involved in the process of gene expression, we have developed several communications and coding theory based models for the process of translation [1-5]. A previous research investigated the use of coding theory based models that quantitatively describe the behavior of the ribosome during translation initiation in prokaryotic organisms [1]. In this paper we have investigated an augmented block code model with modified criteria and assumptions. We have also employed several minimum distance decoders to verify the proposed modified model based on the free energies involved in the binding between the ribosome and the mRNA sequence. The key biological elements considered in forming the investigated model are: the last 13 bases of the 3' end of the 16S rRNA molecule, the common features of bacterial ribosomal binding sites (such as the existence and location of the Shine-Dalgarno sequence), the energies involved in the rRNA-mRNA interaction, and RNA/DNA base-pairing principles. The model was tested on five different E. coli bacterial genomes. The obtained results prove the validity and significance of the model in clearly distinguishing four different test groups of gene predictions. Two of them are based on well known gene finder softwares (e.g. GeneMark [2] and Glimmer [3]).