Fig. 1

Virophage discovery pipeline. a MCP amino acid sequences from reference isolated genomes and published metagenomic contigs were queried against the IMG/VR database with stringent e value cutoffs. All homologous sequences detected were then clustered together to build four independent MCP profiles (HMM models; see details in the “Methods” section). b The resulting four MCP models were used to recruit additional homologous sequences from the entire IMG/M system (containing over 10,000 public samples). All new sequences were clustered, and models were built creating a final set of 15 unique MCP HMMs. c These 15 unique MCP HMMs were then used to search two different databases for homologous sequences: the IMG/M system and a custom assembled human gut database containing 3771 samples from NCBI’s Sequence Read Archive (SRA). d The resulting set of 28,294 non-redundant (NR) sequences (Additional file 1: Table S1) with stringent e value cutoffs was filtered by size and e by the presence of the four core virophage genes (high-quality genomes; HQ virophages). Finally, we predicted completeness of novel metagenomic virophage genomes based on circularity or presence of inverted terminal repeats (ITR)