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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 12, Issue 1

Issues

A web application for automatic prediction of gene translation elongation efficiency

Vladimir S. Sokolov
  • Corresponding author
  • Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Avenue Novosibirsk, 630090, Russian Federation
  • Novosibirsk State University, 2 Pirogova Street Novosibirsk, 630090, Russian Federation
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Bulat S. Zuraev
  • Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Avenue Novosibirsk, 630090, Russian Federation
  • Novosibirsk State University, 2 Pirogova Street Novosibirsk, 630090, Russian Federation
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Sergei A. Lashin
  • Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Avenue Novosibirsk, 630090, Russian Federation
  • Novosibirsk State University, 2 Pirogova Street Novosibirsk, 630090, Russian Federation
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Yury G. Matushkin
  • Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Avenue Novosibirsk, 630090, Russian Federation
  • Novosibirsk State University, 2 Pirogova Street Novosibirsk, 630090, Russian Federation
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-256

Summary

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.

About the article

Published Online: 2016-10-18

Published in Print: 2015-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 1, Pages 16–23, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-256.

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© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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[1]
A. O. Bragin, V. S. Sokolov, P. S. Demenkov, T. V. Ivanisenko, E. Yu. Bragina, Yu. G. Matushkin, and V. A. Ivanisenko
Molecular Biology, 2018, Volume 52, Number 2, Page 279

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