ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database

摘要

BackgroundProphages play a significant role in prokaryotic evolution, often altering the function of the cell that they infect via transfer of new genes e.g., virulence or antibiotic resistance factors, inactivation of existing genes or by modifying gene expression. Recently, phage therapy has gathered renewed interest as a promising alternative to control bacterial infections. Cataloging the repertoire of prophages in large collections of species’ genomes is an important initial step in understanding their evolution and potential therapeutic utility. However, current widely-used tools for identifying prophages within bacterial genome sequences are mainly web-based, can have long response times, and do not scale to keep pace with the many thousands of genomes currently being sequenced routinely.