Investigation of genetic code optimality for overlapping protein coding sequences

An analytical model to determine codon transitions in alternative reading frames based on the statistical properties of prokaryotic genomes within annotated genes is developed. This model predicts the codon usage in alternative reading frames and is applied to study overlapping genes. We investigate the standard genetic code that has a highly nonrandom structure which improves the robustness of the code against several types of errors. A comparison of the standard code with alternative genetic codes is presented investigating if the standard code is optimized to allow long overlapping genes.