This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples.
Is there a "definitive" database used with sequences? How "species-specific" would this be?
Furthermore, are there standard algorithms used to find these MGEs? I suspect we don't have a comprehensive database of all possible MGEs, but it may be possible to query against the sequences we do indeed have (or detect any repetitive elements within the genome).