6533b7d1fe1ef96bd125cc12
RESEARCH PRODUCT
Simulation-based estimation of branching models for LTR retrotransposons
Serge MoulinStéphane ChrétienEmmanuelle LeratChristophe GuyeuxNicolas Seuxsubject
0301 basic medicineStatistics and ProbabilitySource codeTheoretical computer scienceRetroelementsmedia_common.quotation_subjectRetrotransposon[INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE]BiologyBiochemistryGenomeChromosomesBranching (linguistics)[INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing03 medical and health sciences[INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR]SoftwareAnimalsComputer SimulationMolecular BiologyComputingMilieux_MISCELLANEOUSmedia_commoncomputer.programming_languageGeneticsGenomeModels Geneticbusiness.industry[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]Python (programming language)[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM][INFO.INFO-MO]Computer Science [cs]/Modeling and SimulationComputer Science ApplicationsVisualizationComputational Mathematics030104 developmental biologyDrosophila melanogasterComputational Theory and Mathematics[INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA]Programming Languages[INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET]Mobile genetic elements[INFO.INFO-DC]Computer Science [cs]/Distributed Parallel and Cluster Computing [cs.DC]businesscomputerSoftwaredescription
Abstract 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 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. Results 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. Availability and Implementation Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread. Supplementary information are available at Bioinformatics online.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2017-02-01 |