ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY
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 spe...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2015-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/320 |
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| _version_ | 1832575306756521984 |
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| author | V. S. Sokolov B. S. Zuraev S. A. Lashin Yu. G. Matushkin |
| author_facet | V. S. Sokolov B. S. Zuraev S. A. Lashin Yu. G. Matushkin |
| author_sort | V. S. Sokolov |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-7758573bfdd545a8997a846c0d8a1458 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-7758573bfdd545a8997a846c0d8a14582025-02-01T09:58:01ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592015-01-01184/2904909303ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCYV. S. Sokolov0B. S. Zuraev1S. A. Lashin2Yu. G. Matushkin3Institute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaExpression 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.https://vavilov.elpub.ru/jour/article/view/320elongation efficiency indexweb applicationtranslation efficiencysecondary structures |
| spellingShingle | V. S. Sokolov B. S. Zuraev S. A. Lashin Yu. G. Matushkin ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY Вавиловский журнал генетики и селекции elongation efficiency index web application translation efficiency secondary structures |
| title | ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY |
| title_full | ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY |
| title_fullStr | ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY |
| title_full_unstemmed | ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY |
| title_short | ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY |
| title_sort | eloe a web application for estimation of gene translation elongation efficiency |
| topic | elongation efficiency index web application translation efficiency secondary structures |
| url | https://vavilov.elpub.ru/jour/article/view/320 |
| work_keys_str_mv | AT vssokolov eloeawebapplicationforestimationofgenetranslationelongationefficiency AT bszuraev eloeawebapplicationforestimationofgenetranslationelongationefficiency AT salashin eloeawebapplicationforestimationofgenetranslationelongationefficiency AT yugmatushkin eloeawebapplicationforestimationofgenetranslationelongationefficiency |