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Bioinformatics Advance Access published online on June 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl337
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© 2006 The Author(s)
Received April 19, 2006
Revised June 9, 2006
Accepted June 15, 2006

Article

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements

Sébastien Tempel 1, Mathieu Giraud 2, Dominique Lavenier 2, Israël-César Lerman 2, Anne-Sophie Valin 2, Ivan Couée 3, Abdelhak El Amrani 3, and Jacques Nicolas 2 *

1 IRISA-INRIA, Campus de Beaulieu Bât 12, 35042 Rennes cedex, France; CNRS, Université de Rennes 1, UMR 6553 Ecobio, Campus de Beaulieu Bât 14A, 35042 Rennes cedex, France
2 IRISA-INRIA, Campus de Beaulieu Bât 12, 35042 Rennes cedex, France
3 CNRS, Université de Rennes 1, UMR 6553 Ecobio, Campus de Beaulieu Bât 14A, 35042 Rennes cedex, France

* To whom correspondence should be addressed.
Jacques Nicolas, E-mail: DomainOrganizer{at}irisa.fr


  Abstract

Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements, the most complex ones. The dynamics of transposable elements, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of transposable elements. Our method extracts occurrences of a terminus-defined family of transposable elements, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relatively to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains.

Results: Analysis of the new non-autonomous transposable element AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method.

Availability: DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

Associate Editor: Martin Bishop
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