Data From - TE Density: a tool to investigate the biology of transposable elements

Background: Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to theirinherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs’ ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly availablecomputational methods that quantify the presence of TEs relative to genes.
Results: Here, we have developed a tool to more easily quantify TE presence relative to genes through the useof only a gene and TE annotation, yielding a new metric we call TE density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the geno...