Flowchart of profile search using ProPhylo with Double Partial Phylogenetic profiling (DPPP). (A) Search begins with a single query sequence with its BLAST hits. (B) The program then generates a different query profile for each depth in the BLAST hit list. (C) Each of these profiles is then searched against the target genome. (D) The top hits for each of these searches are then collected and the output is presented sorted by significance.