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


BACKGROUND
DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.
Tempel
Sébastien
S
IRISA-INRIA, Campus de Beaulieu Bât 12 35042 Rennes cedex, France.
Giraud
Mathieu
M
Lavenier
Dominique
D
Lerman
Israël-César
IC
Valin
Anne-Sophie
AS
Couée
Ivan
I
Amrani
Abdelhak El
AE
Nicolas
Jacques
J
D000465:Algorithms; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D017343:Genes, Plant; D008390:Markov Chains; D008954:Models, Biological; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements; D010940:Plant Proteins