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 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.
Bergman
Casey M
CM
Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK. casey.bergman@manchester.ac.uk
Quesneville
Hadi
H
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements