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SimulaTE: simulating complex landscapes of transposable elements of populations
MOTIVATION: 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. RESULT...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905622/ https://www.ncbi.nlm.nih.gov/pubmed/29186298 http://dx.doi.org/10.1093/bioinformatics/btx772 |
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author | Kofler, Robert |
author_facet | Kofler, Robert |
author_sort | Kofler, Robert |
collection | PubMed |
description | MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: 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. |
format | Online Article Text |
id | pubmed-5905622 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-59056222018-04-23 SimulaTE: simulating complex landscapes of transposable elements of populations Kofler, Robert Bioinformatics Applications Notes MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: 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. Oxford University Press 2018-04-15 2017-11-27 /pmc/articles/PMC5905622/ /pubmed/29186298 http://dx.doi.org/10.1093/bioinformatics/btx772 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Kofler, Robert SimulaTE: simulating complex landscapes of transposable elements of populations |
title | SimulaTE: simulating complex landscapes of transposable elements of populations |
title_full | SimulaTE: simulating complex landscapes of transposable elements of populations |
title_fullStr | SimulaTE: simulating complex landscapes of transposable elements of populations |
title_full_unstemmed | SimulaTE: simulating complex landscapes of transposable elements of populations |
title_short | SimulaTE: simulating complex landscapes of transposable elements of populations |
title_sort | simulate: simulating complex landscapes of transposable elements of populations |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905622/ https://www.ncbi.nlm.nih.gov/pubmed/29186298 http://dx.doi.org/10.1093/bioinformatics/btx772 |
work_keys_str_mv | AT koflerrobert simulatesimulatingcomplexlandscapesoftransposableelementsofpopulations |