PHACTS: Phage Classification Tool Set

There are two distinct phage lifestyles: lytic and lysogenic. The lysogenic lifestyle has many implications for phage therapy, genomics, and microbiology, however it is often very difficult to determine whether a newly sequenced phage isolate grows lytically or lysogenically just from the genome. Using the ~200 known phage genomes, a supervised random forest classifier was built to determine which proteins of phage are important for determining lytic and lysogenic traits. A similarity vector is created for each phage by comparing each protein from a random sampling of all known phage proteins to each phage genome. Each value in the similarity vector represents the protein with the highest similarity score for that phage genome. This vector is used to train a random forest to classify phage according to their lifestyle. To test the classifier each phage is removed from the data set one at a time and treated as a single unknown. The classifier was able to successfully group 188 of the 196 phages for whom the lifestyle is known, giving my algorithm an estimated 4% error rate. The classifier also identifies the most important genes for determining lifestyle; in addition to integrases, expected to be important, the composition of the phage (capsid and tail) also determines the lifestyle. A large number of hypothetical proteins are also involved in determining whether a phage is lytic or lysogenic.