基于模拟的LTR反转录转座子分支模型估计
Simulation based estimation of branching models for LTR retrotransposons
摘要：
动机：LTR逆转录转座子是一种移动元件，能够像逆转录病毒一样在真核基因组内复制和移动。在目前的工作中，我们提出了一个分支模型来研究这些基因组中的LTR反转录转座子的传播。该模型允许考虑LTR反转录转座子拷贝的位置和降解。在我们的模型中，重复率也被允许随着退化水平而变化。结果：实现了各种功能，以模拟其传播和可视化工具。基于这些模拟工具，我们表明，可以执行该传播模型的参数的准确估计。我们应用这种方法的传播的研究转座因子ROO，GYPSY，和DM 412的染色体上的\textit{Drosophila melanogaster}。可用性：我们的建议已经使用Python软件实现。源代码可以在https://github.com/SergeMOULIN/retrotransposons-spread网站上免费获得。
英文摘要：
Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows to take into account both positions and degradations of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results: Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we show that an accurate estimation of the parameters of this propagation model can be performed. We applied this method to the study of the spread of the transposable elements ROO, GYPSY, and DM412 on a chromosome of \textit{Drosophila melanogaster}. Availability: Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread.
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