Annotating transposable elements in the genome using relational decision tree ensembles

Transposable elements (TEs) are DNA sequences that can change their location within the genome. They contribute to genetic diversity within and across species and their transposing mechanisms may also affect the functionality of genes. Accurate annotation of TEs is an important step towards understanding their effects on genes and their role in genome evolution. We introduce a framework for annotating TEs which is based on relational decision tree learning. It allows to naturally represent the structured data and biological processes involving TEs. Furthermore, it also allows the integration of background knowledge and benefits from the interpretability of decision trees. Preliminary experiments show that our method outperforms two state-of-the-art systems for TE annotation.