danylmb/phage_finder repository overview

⁠Phage_Finder

Fouts DE. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 2006;34(20):5839-51. doi: 10.1093/nar/gkl732. Epub 2006 Oct 24. PMID: 17062630; PMCID: PMC1635311.

Manuscript: https://academic.oup.com/nar/article/34/20/5839/3100473⁠

Software: http://phage-finder.sourceforge.net/⁠

⁠Install & Run

1. docker pull danylmb/phage_finder:v0.1
2. docker run -v /location/of/your/data:/data/MyData --privileged --name phage_finder --tty --init -it danylmb/phage_finder:v0.1 bash
3. /opt/PhageFinder/phage_finder_v2.5_4docker/bin/hmm_blast_trna_aragorn_phagefinder.sh -t annotation.feature_dna.fasta annotation.feature_protein.fasta phage_finder_info.txt /data

⁠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.