Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome

Abstract

Understanding the relationship between transposable elements (TEs) and their clos-est positional genes in the host genome is a key point to explore their poten-tial role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural or-ganization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline which is capable to reveal the positional and directional relationship between TEs and adjacent gene distribution in the host genome. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline.