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Transimulation - protein biosynthesis web service

Siwiak, Marlena and Zielenkiewicz, Piotr (2013) Transimulation - protein biosynthesis web service. PloS one, 8 (9). e73943.. ISSN 1932-6203


Official URL: http://www.plosone.org/article/info%3Adoi%2F10.137...


Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation - a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes' movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.

Item Type:Article
Uncontrolled Keywords:translation, computational model, ribosome traffic, gene expression
Subjects:Q Science > QD Chemistry
Q Science > QH Natural history > QH301 Biology
Divisions:Department of Bioinformatics
ID Code:568
Deposited By: Msc Marlena Siwiak
Deposited On:10 Feb 2014 13:46
Last Modified:15 Oct 2014 11:08

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