Finding prophages in microbial genomes remains a problem with no definitive answer. The majority of existing tools rely on detecting genomic regions enriched in proteins with known phage homologs, which hinders the de novo discovery of phage regions. In this study, a weighted phage detection algorithm, Phage_detector was developed based on seven distinctive characteristics of prophages i.e. protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins. The first five characteristics are capable of identifying prophages without any sequence similarity with known phage genes. Phage_detector locates prophages by ranking genomic regions enriched in distinctive phage traits, which leads to the successful prediction of 92% of prophages (including 33 previously unidentified prophages) in 95 complete bacterial genomes with 8% false negative and 18% false positive.

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.