I have a database with bacterial sequence data that I want to annotate for transposons with respect to antibiotic resistance. After researching the topic, I am more confused as before, as there seem to be a great multitude of divergent transposon families, and I do not know where to start.
Does somebody know any good open source models or tools that could be used for transposon annotation? I know that Pfam is using HMMs for transposon identification, but I do not know how to access those. I have found tools like OASIS or ISFinder for IS annotation, but am unsure how comprehensive those databases are.