Identifying Virus-Like Regions in Microbial Genomes Using Hidden Markov Models

Viruses represent an enormous reservoir of genetic diversity on Earth [1]. Although viruses that infect humans, plant crops, or domesticated livestock have been studied for over a century due to their medical or agricultural importance, there is growing appreciation for the large diversity of viruses that inhabit the biosphere and infect microorganisms such as bacteria, archaea, single-celled eukaryotes, and even other viruses [2–5]. All of these viruses collectively encode a vast diversity of genetic and genomic novelty that is only beginning to be explored, and it represents a major frontier for current and future investigations of biodiversity on the planet.