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Bioinformatics Advance Access originally published online on June 29, 2006
Bioinformatics 2006 22(16):1948-1954; doi:10.1093/bioinformatics/btl337
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

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

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

*To whom correspondence should be addressed.


  Abstract

Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, 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 TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative 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 TE 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/

Contact: DomainOrganizer{at}irisa.fr

Associate Editor: Martin Bishop

Received on April 19, 2006; revised on June 9, 2006; accepted on June 15, 2006

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