title: Simulation-based estimation of branching models for LTR retrotransposons.
abstract: 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 us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level.
  
  
  
  Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation model. We applied this method to the study of the spread of the transposable elements ROO, GYPSY and DM412 on a chromosome of Drosophila melanogaster .
  
  
  
  Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread .
  
  
  
  serge.moulin@univ-fcomte.fr.
  
  
  
  are available at Bioinformatics online.
authors.affiliation: Département d'Informatique des Systèmes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Moulin
authors.affiliation: Laboratoire de Mathématiques de Besançon, UMR 6623 CNRS, Université de Bourgogne Franche-Comté, Besançon, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Seux
authors.affiliation: National Physical Laboratory, Teddington, UK.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Chrétien
authors.affiliation: Département d'Informatique des Systèmes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Guyeux
authors.affiliation: Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Villeurbanne, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lerat
mesh_terms: D000818:Animals; D002875:Chromosomes; D003198:Computer Simulation; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D008957:Models, Genetic; D011381:Programming Languages; D018626:Retroelements; D012984:Software
chemical_list: D018626:Retroelements