By Hammaad Shah
This second semester of Phage Hunting has proven to be very different from the first. I came into this semester knowing that I would be annotating a genome, but not really understanding what that would entail. While I had my concerns at the start, I find myself understanding my task for the next couple of weeks and eager to explore the unique challenges of genomic annotation.
The major dilemma revolved around getting all the tools in place to even begin annotating. The conflict was this: I have a Mac and DNA Master, our DNA annotation program, required Windows. I, personally am used to a Mac interface and am not even remotely comfortable with Windows platforms. Despite this, I found myself looking into different ways to get windows on my Mac and ultimately went with the Bootcamp method. After three hours of struggling with a USB and various downloads, I managed to set up a windows partition on my computer. After installing windows, I realized that I had lost a good 35 GB of storage this process. I remember not being too happy about that, but hoping the annotation process was worth it.
Without a genome to annotate, we spent the first few weeks reading journals and discussing genomics in detail. I was unfamiliar with such journals, and spent a lot of time reading and re-reading. It took more effort on my part than I was used to to glean insights from the readings, and still some technical terms and concepts went over my head. However, the discussion in class was really helpful in getting a better idea of how phage data bases are relevant in understanding phage phylogeny and development.
When the genome for Phatniss finally came in, the class became much more engaging. Finally, we would be able to do something ourselves, just as we had the first semester. After some hiccups with getting DNA Master set up, I managed to understand the process for annotation. There are a lot of things to learn, but it’s manageable with the guide we have. After practicing on the first ten genes, I have a much better grasp on the nuances of annotation. There’s no clear cut solution, but rather a systematic consideration of multiple factors.
As of now, I have my genes to annotate assigned to me, but have not yet completed the annotation. It is slightly daunting to begin this process, but then again so was working in the lab first semester. Things seem to be looking up in Phage Hunting’s spring semester, and I hope I find DNA annotation as rewarding as isolating a phage.