prophet

ProphET is a Linux-based software tool that efficiently identifies prophages within bacterial genome sequences. Prophages are integrated viral genomes that can alter the function of their host cells by transferring new genes, inactivating existing genes, or modifying gene expression. Identifying prophages is crucial for understanding their evolutionary impact and potential therapeutic applications, such as phage therapy.

ProphET addresses the limitations of current web-based prophage prediction tools, which can have long response times and do not scale well with the increasing number of sequenced genomes. The tool inputs a bacterial genome sequence in FASTA format and its corresponding gene annotation in GFF. It then identifies prophages in three steps:

1. Similarity search: ProphET compares the input genome against a database of known prophage genes.

2. Calculation of prophage gene density: The tool assesses the density of prophage genes within the genome.

3. Edge refinement: ProphET refines the boundaries of the identified prophage regions.