Discovering and detecting transposable elements in genome sequences

The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotateTEs in the post-genomic era, covering both the discovery of newTE families and the detection of individual TE copies in genome sequences.These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods.We conclude that the integration and visuali-zation of multiple approaches and the development of new conceptual representations forTE annotation will further advance the computational analysis of this dynamic component of the genome