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Briefings in Bioinformatics Advance Access published online on October 10, 2007
Briefings in Bioinformatics, doi:10.1093/bib/bbm048
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Discovering and detecting transposable elements in genome sequences

Casey M. Bergman and Hadi Quesneville

Corresponding author. Casey M. Bergman, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. Tel: +44 (0)161-275-1713; Fax: +44 (0)161-275-5082; E-mail: casey.bergman{at}manchester.ac.uk

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 annotate TEs in the post-genomic era, covering both the discovery of new TE 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 visualization of multiple approaches and the development of new conceptual representations for TE annotation will further advance the computational analysis of this dynamic component of the genome.

Keywords: transposable element, genome annotation, repetitive DNA, bioinformatics

Submitted: July 16, 2007. Accepted: September 17, 2007.


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