The Annotation of the partial genome of the Bacteriophage Stagni with the use of programs DNA Master and Virtual Machine

Elinsky, Amber, Christopher Harness, Joshua Thomson, and Jacob Kagey

The Siphoviridae mycobacteriophage Stagni was isolated and annotated from a soil sample using the principles and guidance of the HHMI SEA-Phage program. The SEA Phages program allows undergraduate students worldwide to get involved in the studies of genetics through the observation and annotation of bacteriophage genomes. The importance of this research lies in the attempt to combat multidrug resistant strands of bacteria. Since mycobacteriophage are a form of virus that targets bacteria cells specifically, the use of phage therapy is being considered to help combat the rise in antibiotic resistance. Stagni’s initial gene placement was predicted through the auto annotation program DNA Master after this data was received from University of Pittsburgh. Using additional information provided by coding files from the Glimmer and GeneMark programs and online BLAST databases, we were able to check the predictions and placements made from DNA Master and Virtual Machine in order to identify and compare each gene section to other well-known structures of different phage. Out of the ninety sequenced genes picked up by DNA Master, forty-four were successfully annotated (from sections A and C), having genes modified and added into the program after comparisons with other research groups. Although the structures of Stagni have been determined, the functions of these proteins are currently unknown, opening up further explorations into other research opportunities such as the infections of other bacteria.