{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,18]],"date-time":"2023-09-18T01:18:28Z","timestamp":1694999908271},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"NMS\/IRD","award":["117480"],"award-info":[{"award-number":["117480"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Our proposal has been implemented using Python software. Source code is freely available on the web at https:\/\/github.com\/SergeMOULIN\/retrotransposons-spread.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw622","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"320-326","source":"Crossref","is-referenced-by-count":1,"title":["Simulation-based estimation of branching models for LTR retrotransposons"],"prefix":"10.1093","volume":"33","author":[{"given":"Serge","family":"Moulin","sequence":"first","affiliation":[{"name":"D\u00e9partement d\u2019Informatique des Syst\u00e8mes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"Nicolas","family":"Seux","sequence":"additional","affiliation":[{"name":"Laboratoire de Math\u00e9matiques de Besan\u00e7on, UMR 6623 CNRS, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"St\u00e9phane","family":"Chr\u00e9tien","sequence":"additional","affiliation":[{"name":"National Physical Laboratory, Teddington, UK"}]},{"given":"Christophe","family":"Guyeux","sequence":"additional","affiliation":[{"name":"D\u00e9partement d\u2019Informatique des Syst\u00e8mes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"Emmanuelle","family":"Lerat","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire Biom\u00e9trie et Biologie Evolutive, Villeurbanne, France"}]}],"member":"286","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"key":"2023020204403506500_btw622-B1","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1126\/science.287.5461.2185","article-title":"The genome sequence of Drosophila melanogaster","volume":"287","author":"Adams","year":"2000","journal-title":"Science"},{"key":"2023020204403506500_btw622-B2","doi-asserted-by":"crossref","first-page":"R22","DOI":"10.1186\/gb-2009-10-2-r22","article-title":"Widespread evidence for horizontal transfer of transposable elements across drosophila genomes","volume":"10","author":"Bartolom\u00e9","year":"2009","journal-title":"Genome Biol"},{"key":"2023020204403506500_btw622-B3","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1101\/gr.5558208","article-title":"Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health","volume":"18","author":"Belancio","year":"2008","journal-title":"Genome Res"},{"key":"2023020204403506500_btw622-B4","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/1471-2148-9-205","article-title":"Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete drosophila genomes","volume":"9","author":"De la Chaux","year":"2009","journal-title":"BMC Evol. 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