The P2RP workflow. If users upload a nucleotide sequence query there is an initial gene-prediction step to yield protein sequences for analysis. Protein sequences (whether predicted by P2RP or inputted by the user), are then screened for the presence of developer-specified sets of conserved domains using SMART and Pfam domain profiles. Proteins with hits to appropriate domain profiles are then used to populate a ‘P2RP Database’. Assignment of P2RP Database proteins to specific categories and sub-categories of RPs is then achieved using ‘Domains combination and classification’ algorithms. The results of the RP analysis can then be viewed as an interactive webpage or exported in a user-defined format.