EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes

Horizontal transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. Genetic elements derived from horizontal transfer are known as Endogenous Bacterial Elements and Endogenous Viral Elements. Endogenous elements characterization provides a snapshot of past host-pathogen interactions and coevolution as well as a reference sequence information to remove false positive results from viral metagenomic studies. However, there is a current lack of standardized tools for endogenous elements identification, which hinder comparative studies and reproducibility within this field. Here we describe EEfinder, a new tool for identification and classification of endogenous elements derived from horizontal transfer. The tool was developed to include six standard steps performed in this type of analysis: data cleaning, pairwise alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder can systematically identify endogenous elements with bacterial/viral origin.