Protein sequences from genomes and metagenomes were clustered and aligned to produce de novo protein profiles. De novo profiles and profiles obtained from public databases were then clustered, and cluster representatives were selected to reduce redundancy. In parallel, reference chromosome, plasmid and virus sequences were clustered into RCs. Sequences were then weighed in such a way that the sum of the weights within each RC was constant. Representative protein profiles were mapped to reference sequences, and chromosome-, plasmid- and virus-specificity metrics were computed for each profile based on the weighed number of hits to sequences of each class. Markers that were highly specific to one of the three classes were then selected. The position of each selected marker (circles) in the ternary plot is determined by its specificity, and the colors represent the marker density in a region.
