Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.
Bioinformatics
; 22(16): 1948-54, 2006 Aug 15.
Article
en En
| MEDLINE
| ID: mdl-16809391
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/.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Elementos Transponibles de ADN
/
Análisis de Secuencia de ADN
/
Biología Computacional
Tipo de estudio:
Health_economic_evaluation
/
Risk_factors_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2006
Tipo del documento:
Article
País de afiliación:
Francia