A web application for automatic prediction of gene translation elongation efficiency
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 Efficie...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2015-03-01
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| Series: | Journal of Integrative Bioinformatics |
| Online Access: | http://www.degruyter.com/view/j/jib.2015.12.issue-1/jib-2015-256/jib-2015-256.xml?format=INT |
| _version_ | 1819261814385410048 |
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| author | Sokolov Vladimir S. Zuraev Bulat S. Lashin Sergei A. Matushkin Yury G. |
| author_facet | Sokolov Vladimir S. Zuraev Bulat S. Lashin Sergei A. Matushkin Yury G. |
| author_sort | Sokolov Vladimir S. |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T19:47:47Z |
| format | Article |
| id | doaj.art-d424c9aff2f648159742ce7f25531aec |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-23T19:47:47Z |
| publishDate | 2015-03-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-d424c9aff2f648159742ce7f25531aec2022-12-21T17:33:30ZengDe GruyterJournal of Integrative Bioinformatics1613-45162015-03-01121162310.1515/jib-2015-256jib-2015-256A web application for automatic prediction of gene translation elongation efficiencySokolov Vladimir S.0Zuraev Bulat S.1Lashin Sergei A.2Matushkin Yury G.3Institute of Cytology and Genetics SB RAS, 10 Lavrentieva AvenueNovosibirsk, 630090, Russian FederationInstitute of Cytology and Genetics SB RAS, 10 Lavrentieva AvenueNovosibirsk, 630090, Russian FederationInstitute of Cytology and Genetics SB RAS, 10 Lavrentieva AvenueNovosibirsk, 630090, Russian FederationInstitute of Cytology and Genetics SB RAS, 10 Lavrentieva AvenueNovosibirsk, 630090, Russian FederationExpression 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.http://www.degruyter.com/view/j/jib.2015.12.issue-1/jib-2015-256/jib-2015-256.xml?format=INT |
| spellingShingle | Sokolov Vladimir S. Zuraev Bulat S. Lashin Sergei A. Matushkin Yury G. A web application for automatic prediction of gene translation elongation efficiency Journal of Integrative Bioinformatics |
| title | A web application for automatic prediction of gene translation elongation efficiency |
| title_full | A web application for automatic prediction of gene translation elongation efficiency |
| title_fullStr | A web application for automatic prediction of gene translation elongation efficiency |
| title_full_unstemmed | A web application for automatic prediction of gene translation elongation efficiency |
| title_short | A web application for automatic prediction of gene translation elongation efficiency |
| title_sort | web application for automatic prediction of gene translation elongation efficiency |
| url | http://www.degruyter.com/view/j/jib.2015.12.issue-1/jib-2015-256/jib-2015-256.xml?format=INT |
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