Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.

Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5' side of the D loop, the 3' side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.