Transposable element annotation using relational random forests

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 present a framework for annotating TEs which is based on relational random forests. It allows to naturally represent the structured data and biological processes involving TEs. Furthermore, it allows the integration of background knowledge.