title: VisualTE: a graphical interface for transposable element analysis at the genomic scale.
abstract: BACKGROUND
  Transposable elements are mobile DNA repeat sequences, known to have high impact on genes, genome structure and evolution. This has stimulated broad interest in the detailed biological studies of transposable elements. Hence, we have developed an easy-to-use tool for the comparative analysis of the structural organization and functional relationships of transposable elements, to help understand their functional role in genomes.
  
  
  RESULTS
  We named our new software VisualTE and describe it here. VisualTE is a JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable elements and genomic information from annotation and repeat data. Result analyses are displayed in several graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes' features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms.
  
  
  CONCLUSIONS
  VisualTE graphical interface makes possible comparative analyses of transposable elements in any annotated sequence as well as structural organization and functional relationships between transposable elements and other genetic object. This tool is freely available at: http://lcb.cnrs-mrs.fr/spip.php?article867 .
authors.affiliation: Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, 13402, France. sebastien.tempel@univ-amu.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tempel
authors.affiliation: Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, 13402, France. talla@imm.cnrs.fr.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Talla
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D023281:Genomics; D020407:Internet; D012984:Software
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements