Simulation based estimation of branching models for LTR retrotransposons

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.Comment: 7 pages, 3 figures, 7 tables. Submit to "Bioiformatics" on March 1, 201