By Billy Lu
Second semester started out entirely different from the first. In the beginning of the first semester, we were thrown into a laboratory environment and followed a procedure to isolate a pure phage population and extract its DNA. This semester is much less hands on and more analytical.
During the super long wait for sequencing of Phatniss, I learned that we had to use programs called Phamerator and DNA Master. Phamerator is a genome exploration tool and DNA Master is used to study and annotate genes of a sequence. I had to install an emulator called Virtual Box to run Ubuntu in order to run Phamerator. Apparently everyone had to do this. We didn’t do much with Phamerator and I hope to learn more about it. Also, I don’t get why so many people says Macs are so much than Windows. If someone says that to me next time, I respond, “But can you run DNA Master?” While Mac users were scrambling to install Windows, I calmly downloaded DNA Master, which contains its own share of problems. It was difficult to BLAST all of the genes at once and it froze a lot. Even so, I learned to annotate (mostly) the genes of Phatniss when the genome finally arrived.
Later in the semester, the class will be performing their own experiments. I plan on finding substances that can disrupt the membrane of mycobacteria and decrease binding of mycobacteriophages to it. While I waiting to do that, I am in the process of annotating a part of the Phatniss genome this spring break. Hopefully, I will be able to finish it and work more with Phamerator.