EloE: Web application for estimation of gene translation elongation efficiency

Abstract

Many modern investigations study important gene characteristic such as the efficiency of its expression. As is known, it is determined at the levels of transcription, translation, posttranslational modification, etc. The EloE (Elongation Efficiency) program, which sorts the organism genes in order of decreasing their supposed translation elongation rate based on the analysis of their nucleotide sequences, is presented in the work. The obtained theoretical data are significantly correlated to the available experimental data on gene expression in different organisms (for example, S. cerevisiae and H. pylori). The program also detects preferential codons in the organism genome and constructs the distribution of the stability of potential secondary structures near the mRNA 5′- and 3′-ends. The program can be used for preliminarily estimating the level of gene expression in the studied organism (for which the experimental data are not available yet). The results of EloE can be transferred in third-party program instruments that model artificial genetic constructions for genetically engineered experiments.