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Transposable elements

The two main pipelines of the REPET package are dedicated to the detection, annotation and analysis of transposable elements in genomic sequences. With these tools, we obtained data for various genomes. Some results and data are available below.

REPETDB is a database of transposable elements. Reference sequences for various species are stored with the Intermine data warehouse framework.
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Data used for the genome paper of the Drosophila 12 Genomes Consortium: Clark AG, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8; 450(7167):203-18. PMID: 17994087 
  • BLASTER/TBLASTX  results with BDGP TE ...
Data from Buisine, Quesneville and Colot (Genomics 2008) used to annotate the transposable elements (TEs) of the A. thaliana genome (release 5). Annotation are available on TAIR web site.
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The transposable element reference sequences for the Ectocarpus silicosus genome have been obtained with the REPET package and were manually curated. The results are published in the Ectocarpus genome paper.
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We annotated transposable elements in Acyrthosiphon pisum (pea aphid) in the frame of the International Aphid Genomic Consortium (IAGC).
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In the framework of several international genome sequencing projects, we have analyzed the transposable element (TE) content of several fungal genomes using the REPET package.You can download TE consensus library and genome annotation files (GFF) at: https://urgi.versailles.inra.fr/download/fungi/TEs/ Leptosphaeria ...
Update: 12 Mar 2013
Creation date: 21 Jun 2010