Bacteriophages are viruses that infect and kill bacteria. With antibiotic resistance becoming a larger problem, phage therapy is being considered as a treatment alternative. However, we still need to learn more about phages before we can market them as a safe product. The current standards of phage annotation only identify roughly ~30% of protein functions, leaving the rest as No Known Function. Without knowing what those proteins do, we cannot safely use phage therapy. A possible method of phage regulation involves determining therapeutically equivalent phages based on their statistically significant proteins. Then a database of equivalent phages could be built. However, with ~70% NKF proteins, there is still too much unknown. I propose a new method of protein assignment using alignment programs, hidden Markov models, cellular location predictions, and simulations. The NKF proteins within the genome PotatoSplit dropped from 63% to 37%, with the majority of new proteins being proteins related to phage structure.