Program > Browse abstracts by author > Robert Hubley

The display of transposable elements and their systematic annotation across the thousands of new genomes is a neglected topic in the genomic database ecosystem. The Repeatmasker team and the UCSC Genome Browser group have been working to remedy this. 

1) The Browser has a special display mode for RepeatMasker output, available on the human genome, that shows the size of the Repeatmasker query sequence and how the individual pieces of e.g. L1 elements were joined together.

2) Most of the thousands of NCBI assemblies added to the UCSC GenArk collection of genome browsers at https://hgdownload.soe.ucsc.edu/hubs/ were processed with both repeatmodeler and Repeatmasker, and both annotations are available for download and analysis. All VGP (Vertebrate Genome Project) assemblies have been processed like this and a selected set of other assemblies and we can run repeatmodeler on any other set of assemblies on request.

3) The UCSC Repeatbrowser https://repeatbrowser.ucsc.edu/ can show a consensus sequences for each repeat type in the human reference genome and projects various annotations (genes, ENCODE, Chip-Seq) to these consensus sequences. 

We present these tools in the hope that they help make transposable elements acessible to a larger audience. We also are looking for feedback on the annotation and display of TE annotations on the Genome Browser.