Identifying False Positive Genes of the ThreeRngTarjay Genome

McMahon, Diana, Angelina Antonyan, Stephanie B. Conant, Jonathan S. Finkel, and Jacob D. Kagey

Bacteriophages are viruses that infect and lyse bacteria and have the potential to replace antibiotics, which is crucial due to antibiotic resistance. ThreeRngTarjay, a siphoviridae Cluster J bacteriophage, was annotated to contribute to the University of Pittsburgh's Science Education Alliance program (SEA-PHAGES). In annotating a portion of the bacteriophage ThreeRngTarjay’s genome, it was determined that some genes claimed by DNA Master were not present. A total of four predicted genes ‒genes 112, 129, 149, and 201‒ out of 69 genes were detected to be false positive genes based on certain criteria. One criterion includes if the gene has contrasting transcription direction. Other evidence for a false positive gene is if the gene has excessive overlap with adjacent genes. BLAST data was examined to see if the gene had similar genomic sequencing and precise alignment with other known mycobacteriophage. Another indicator for gene deletions include the final RBS score highly diverging from zero. A lack of coding potential, delineated by the software Genemark and GLIMMER, was considered evidence to remove the predicted genes from DNA Master. Programs used in analysis include Glimmer, Genemark, and DNA Master. Web-based information was provided by phagesdb.org and ncbi.gov using a Basic Local Alignment Search Tool (BLAST).