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- DOI: 10.4161/mge.19479
- PMID: 22754753
- UKPMCID: 22754753
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A proposal for the reference-based annotation of de novo transposable element insertions.
Mobile genetic elements. 2012;2(1):51-54.
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Full-text held externally
- DOI: 10.4161/mge.19479
- PMID: 22754753
- UKPMCID: 22754753
Abstract
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.