A web application for automatic prediction of gene translation elongation efficiency

• Published in: Journal of integrative bioinformatics Vol. 12; no. 1; pp. 16 - 23
• Main Authors: Sokolov, Vladimir S., Zuraev, Bulat S., Lashin, Sergei A., Matushkin, Yury G.
• Format: Journal Article
• Language: English
• Published: Germany De Gruyter 01.03.2015
• ISSN: 1613-4516; 1613-4516
• DOI: 10.1515/jib-2015-256

Expression efficiency is one of the major characteristics describing genes in various modern investigations. Expression efficiency of genes is regulated at various stages: transcription, translation, posttranslational protein modification and others. In this study, a special EloE (Elongation Efficiency) web application is described. The EloE sorts the organism’s genes in a descend order on their theoretical rate of the elongation stage of translation based on the analysis of their nucleotide sequences. Obtained theoretical data have a significant correlation with available experimental data of gene expression in various organisms. In addition, the program identifies preferential codons in organism’s genes and defines distribution of potential secondary structures energy in 5´ and 3´ regions of mRNA. The EloE can be useful in preliminary estimation of translation elongation efficiency for genes for which experimental data are not available yet. Some results can be used, for instance, in other programs modeling artificial genetic structures in genetically engineered experiments. The EloE web application is available at http://www-bionet.sscc.ru:7780/EloE.