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Open Access Research article

ModuleOrganizer: detecting modules in families of transposable elements

Sebastien Tempel1, Christine Rousseau2, Fariza Tahi1 and Jacques Nicolas3*

Author Affiliations

1 IBISC, Tour Evry 2, 523, place des terrasses del'agora, 91000 Evry, France

2 INP-ENSAT, Avenue de l'agrobiopole 31326 Castanet tolosan, France

3 IRISA-INRIA, Campus de Beaulieu, bât 12, 35042 Rennes cedex, France

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BMC Bioinformatics 2010, 11:474  doi:10.1186/1471-2105-11-474

Published: 22 September 2010

Abstract

Background

Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification of these transformations remains a difficult issue. The study of families of transposable elements is generally founded on a multiple alignment of their sequences, a critical step that is adapted to transposons containing mostly localized nucleotide mutations. Many transposons that have lost their protein-coding capacity have undergone more complex rearrangements, needing the development of more complex methods in order to characterize the architecture of sequence variations.

Results

In this study, we introduce the concept of a transposable element module, a flexible motif present in at least two sequences of a family of transposable elements and built on a succession of maximal repeats. The paper proposes an assembly method working on a set of exact maximal repeats of a set of sequences to create such modules. It results in a graphical view of sequences segmented into modules, a representation that allows a flexible analysis of the transformations that have occurred between them. We have chosen as a demonstration data set in depth analysis of the transposable element Foldback in Drosophila melanogaster. Comparison with multiple alignment methods shows that our method is more sensitive for highly variable sequences. The study of this family and the two other families AtREP21 and SIDER2 reveals new copies of very different sizes and various combinations of modules which show the potential of our method.

Conclusions

ModuleOrganizer is available on the Genouest bioinformatics center at http://moduleorganizer.genouest.org webcite