title: Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.
abstract: 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.
authors.affiliation: The Institute for Genomic research, 9712 Medical Center Drive, Rockville, MD 20850, USA. dfouts@tigr.org
authors.forename: Derrick E
authors.initials: DE
authors.lastname: Fouts
mesh_terms: D001287:Attachment Sites, Microbiological; D019295:Computational Biology; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D020407:Internet; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D039002:Prophages / Q000145:classification* / Q000235:genetics*; D012329:RNA, Bacterial / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D012984:Software
chemical_list: D012329:RNA, Bacterial; C096222:tmRNA; D012343:RNA, Transfer