2 research outputs found
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,
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