{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T12:28:09Z","timestamp":1773491289061,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,11,27]],"date-time":"2017-11-27T00:00:00Z","timestamp":1511740800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["P29016"],"award-info":[{"award-number":["P29016"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SimulaTE is implemented in Python and available at https:\/\/sourceforge.net\/projects\/simulates\/. Manual https:\/\/sourceforge.net\/p\/simulates\/wiki\/Home\/#manual; Test data and tutorials https:\/\/sourceforge.net\/p\/simulates\/wiki\/Home\/#walkthrough; Validation https:\/\/sourceforge.net\/p\/simulates\/wiki\/Home\/#validation.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx772","type":"journal-article","created":{"date-parts":[[2017,11,25]],"date-time":"2017-11-25T12:08:50Z","timestamp":1511611730000},"page":"1419-1420","source":"Crossref","is-referenced-by-count":7,"title":["SimulaTE: simulating complex landscapes of transposable elements of populations"],"prefix":"10.1093","volume":"34","author":[{"given":"Robert","family":"Kofler","sequence":"first","affiliation":[{"name":"Institute f\u00fcr Populationsgenetik, Vetmeduni Vienna, Wien, Austria"}]}],"member":"286","published-online":{"date-parts":[[2017,11,27]]},"reference":[{"key":"2023012713010828200_btx772-B1","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1111\/mec.12170","article-title":"The impact of transposable elements in environmental adaptation","volume":"22","author":"Casacuberta","year":"2013","journal-title":"Mol. Ecol"},{"key":"2023012713010828200_btx772-B2","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrn3730","article-title":"Mobile DNA elements in the generation of diversity and complexity in the brain","volume":"15","author":"Erwin","year":"2014","journal-title":"Nat. Rev. Neurosci"},{"key":"2023012713010828200_btx772-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13100-015-0055-3","article-title":"Transposable element detection from whole genome sequence data","volume":"6","author":"Ewing","year":"2015","journal-title":"Mobile DNA"},{"key":"2023012713010828200_btx772-B4","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1126\/science.1089670","article-title":"Mobile elements: drivers of genome evolution","volume":"303","author":"Kazazian","year":"2004","journal-title":"Science"},{"key":"2023012713010828200_btx772-B5","doi-asserted-by":"crossref","first-page":"e1002487","DOI":"10.1371\/journal.pgen.1002487","article-title":"Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster","volume":"8","author":"Kofler","year":"2012","journal-title":"PLoS Genet"},{"key":"2023012713010828200_btx772-B6","first-page":"2759","article-title":"PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq","author":"Kofler","year":"2016"},{"key":"2023012713010828200_btx772-B7","first-page":"589","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012713010828200_btx772-B8","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1534\/g3.117.043893","article-title":"McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole Genome Shotgun Sequencing Data","volume":"7","author":"Nelson","year":"2017","journal-title":"G3 Genes Genomes Genet"},{"key":"2023012713010828200_btx772-B9","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1126\/science.274.5288.765","article-title":"Nested retrotransposons in the intergenic regions of the maize genome","volume":"274","author":"SanMiguel","year":"1996","journal-title":"Science"},{"key":"2023012713010828200_btx772-B10","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/nrg3803","article-title":"Sequencing pools of individuals\u2014mining genome-wide polymorphism data without big funding","volume":"15","author":"Schl\u00f6tterer","year":"2014","journal-title":"Nat. Rev. Genet"},{"key":"2023012713010828200_btx772-B11","doi-asserted-by":"crossref","first-page":"e28297","DOI":"10.7554\/eLife.28297","article-title":"Resolving the prevalence of somatic transposition in Drosophila","volume":"6","author":"Treiber","year":"2017","journal-title":"eLife"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/8\/1419\/48915414\/bioinformatics_34_8_1419.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/8\/1419\/48915414\/bioinformatics_34_8_1419.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T06:07:58Z","timestamp":1693289278000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/8\/1419\/4665422"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,27]]},"references-count":11,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2018,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx772","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,4,15]]},"published":{"date-parts":[[2017,11,27]]}}}