ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database

Prophages are a significant force in prokaryote evolution. The remaining sequences of a bacteriophage integration event are known for altering gene expression, enabling creative destruction of the bacterial genome and to induce pathogenicity by harboring and transposing virulence and antibiotic resistance factors. In the light of the dreadful expansion of antibiotic resistance bacteriophages have gathered renewed interest from the scientific community and public health decision makers as a promising long forgotten alternative to control bacterial infections. Cataloging the repertoire of prophages and their integration sites is an important initial step in the understanding of bacteriophages either as tool or as a threat. In this work, we present ProphET (Prophage Estimation Tool), a standalone application without the limitations of their web based counterparts and which identifies prophages in bacterial genomes with higher precision than similar applications.