Today we worked on an abstract for our research project:

Analysis of Alternative Clustering Methods for Arthrobacteriophages

Abstract: The study of bacteriophages includes an investigation of their DNA. An important aspect of DNA analysis is clustering, the means by which discovered bacteriophages are sorted according to genome similarity. The current method for clustering is an analysis and comparison of a bacteriophage’s full genome. However, this presents several limitations for clustering, as it requires the completion of full-genome sequencing and the production of a high-titer DNA lysate. In the interest of easing the clustering process, additional clustering methods were analyzed including sorting by G/C content and clustering by Tape Measure Proteins (TMP). Through comparison to existing clusters, it was determined that the G/C content of phage clusters group too closely to be useful for clustering. However, through the use of a Gepard dotplot, it was determined that there is enough similarity among TMPs within clusters and enough diversity between clusters to facilitate that clustering method. From this, we used cluster TMP alignments generated by Mega7 to find conserved regions within each genome. From these, small PCR primers were created that were specific to each cluster’s TMP with minimal off-target similarity. These will allow future researchers to determine the clusters of bacteriophages with a minimal sample of DNA earlier in the process without going through whole genome sequencing. In conclusion, TMP analysis is a highly effective alternative clustering method with the added benefit of PCR primers, which offer the benefits of less lab work and the ability to sort phages with a low titer DNA lysate.