Flowchart for profile search using ProPhylo with the Partial Phylogenetic Profile algorithm (PPP). For each step, the relevant software name is indicated. (A) Creation of a profile from various search methods or directly using a set of GenBank GIs. (B) The created profile is a tab delimited text file containing a set of taxonomic IDs from NCBI taxonomic database and 1's and 0's for the presence and absence of the query protein family. (C) The main script ppp.pl searches a given genome using the query profile and generates results as a ranked list of candidate functionally linked proteins.