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A proposal for the reference-based annotation of de novo transposable element insertions

Understanding the causes and consequences of transposable element (TE) activity in the genomic era requires sophisticated bioinformatics approaches to accurately identify individual insertion sites. Next-generation sequencing technology now makes it possible to rapidly identify new TE insertions usi...

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Detalles Bibliográficos
Autor principal: Bergman, Casey M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Landes Bioscience 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383450/
https://www.ncbi.nlm.nih.gov/pubmed/22754753
http://dx.doi.org/10.4161/mge.19479
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author Bergman, Casey M.
author_facet Bergman, Casey M.
author_sort Bergman, Casey M.
collection PubMed
description Understanding the causes and consequences of transposable element (TE) activity in the genomic era requires sophisticated bioinformatics approaches to accurately identify individual insertion sites. Next-generation sequencing technology now makes it possible to rapidly identify new TE insertions using resequencing data, opening up new possibilities to study the nature of TE-induced mutation and the target site preferences of different TE families. While the identification of new TE insertion sites is seemingly a simple task, the mechanisms of transposition present unique challenges for the annotation of de novo transposable element insertions mapped to a reference genome. Here I discuss these challenges and propose a framework for the annotation of de novo TE insertions that accommodates known mechanisms of TE insertion and established coordinate systems for genome annotation.
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spelling pubmed-33834502012-06-29 A proposal for the reference-based annotation of de novo transposable element insertions Bergman, Casey M. Mob Genet Elements Commentary Understanding the causes and consequences of transposable element (TE) activity in the genomic era requires sophisticated bioinformatics approaches to accurately identify individual insertion sites. Next-generation sequencing technology now makes it possible to rapidly identify new TE insertions using resequencing data, opening up new possibilities to study the nature of TE-induced mutation and the target site preferences of different TE families. While the identification of new TE insertion sites is seemingly a simple task, the mechanisms of transposition present unique challenges for the annotation of de novo transposable element insertions mapped to a reference genome. Here I discuss these challenges and propose a framework for the annotation of de novo TE insertions that accommodates known mechanisms of TE insertion and established coordinate systems for genome annotation. Landes Bioscience 2012-01-01 /pmc/articles/PMC3383450/ /pubmed/22754753 http://dx.doi.org/10.4161/mge.19479 Text en Copyright © 2012 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Commentary
Bergman, Casey M.
A proposal for the reference-based annotation of de novo transposable element insertions
title A proposal for the reference-based annotation of de novo transposable element insertions
title_full A proposal for the reference-based annotation of de novo transposable element insertions
title_fullStr A proposal for the reference-based annotation of de novo transposable element insertions
title_full_unstemmed A proposal for the reference-based annotation of de novo transposable element insertions
title_short A proposal for the reference-based annotation of de novo transposable element insertions
title_sort proposal for the reference-based annotation of de novo transposable element insertions
topic Commentary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383450/
https://www.ncbi.nlm.nih.gov/pubmed/22754753
http://dx.doi.org/10.4161/mge.19479
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