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. 2013 Sep 5;8(9):e73943.
doi: 10.1371/journal.pone.0073943. eCollection 2013.

Transimulation - protein biosynthesis web service

Marlena Siwiak  1 , Piotr Zielenkiewicz
Affiliations

Transimulation - protein biosynthesis web service

Marlena Siwiak et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Translation speed plot generated by Transimulation.
An example plot of translation speed (in aa/sec) in relation to the coding sequence of one of the E.coli genes. To facilitate analysis, the plot was smoothed by calculating translation speed over a 10-codon sliding window. Similar plots for window sizes of 1, 2, 5, 10, 20, 30, and 50 codons are generated for all analyzed genes and sequences uploaded by the user.
Figure 2
Figure 2. Calculated protein abundance vs experimental studies.
Correlations between protein abundances calculated in our model (as formula image times formula image) and those obtained in experimental studies , –; n – sample size, formula image – Spearman correlation coefficient and its 95% confidence interval.
See this image and copyright information in PMC

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