ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY
Abstract
Expression efficiency is one of major characteristics of genes considered in a number of modern investigations. It is known that gene expression efficiency in an organism is regulated at many stages: transcription, translation, posttranslational protein modification, and others. In this study, a special EloE (Elongation Efficiency) web application is described. It sorts genes in an organism in the order of decreasing theoretical rate of the elongation stage of translation deduced from their nucleotide sequences. The predictions done in this way show a significant correlation with available experimental data on gene expression in various organisms, for instance, S. cerevisiae and H. pylori. In addition, the program identifies preferential codons in a genome and defines the distribution of stability of potential secondary structures in 5′ and 3′ regions of mRNA. EloE can be useful in preliminary estimation of translation elongation efficiency of genes in organisms for which experimental data are not available yet. Some results can be used, for instance, in other programs modeling artificial genetic constructs in gene engineering experiments.
About the Authors
V. S. Sokolov
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Russian Federation
Russian Federation
B. S. Zuraev
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
S. A. Lashin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
Yu. G. Matushkin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Novosibirsk National Research State University, Novosibirsk, Russia
Russian Federation
Russian Federation
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