By Marissa Totten
So probably one of the most important, non-biology, things I’ve learned this past semester is to NEVER under ANY circumstances trust that a program will actually save your work. Honestly, from now on I’m saving my documents as a new file every ten minutes. Why? Three letters and one word: DNA Master. This program made me absolutely certain that I never want to go into tech support. EVER. The problems first started with forgetting to hit post, Hunter, before moving onto another gene. Then want on to display errors that requested sums as high as $2800, Ashley. Then the best message that could pop up was the one that notified you that your previous file could not be opened. Great. Countless gene blasts lost, new ORF starts erased, and time spent waiting on HHpred function blasts (most of them turned up no known functions anyway) wasted. Word to the wise: save a new file after every couple of annotated genes. Do it. After plenty of corrupt files and the phrase “I swear I finished the annotation,” I’ve learned my lesson. I currently have 55 Phatniss files saved. After all of this, I honestly think that annotating by hand is the best way to go. It’s actually a lot faster because you don’t have to keep switching tabs and the only way you’re going to lose your data is by losing the papers yourself. Despite all of the annoyance and frustration this program presented, annotating is a really cool process! It was a great look into what genetics entail and what scientists have to go through to figure out gene functions.
But now we’ve started the best part of the course, of course: web lab experiments! The hands-on work in this class is the best. I’ll admit my experiment isn’t the most interesting, I wrote it up the day before it was due while I was at a soccer tournament, but I’m still super excited to be working with my phage Drac109 again (despite the fact that I have to count and measure 150-300 plaques every class). I plan on switching the top agar with agarose because agarose doesn’t contain sulfates and other molecules that are suppose to inhibit virus propagation. Proven by the entire lab last semester, many phage aren’t bother by these molecules in the top agar in the first place, so it’s possible that the agarose will actually allow plaque size to increase. Agarose doesn’t have the same nutritional content as top agar though, so I may have to throw a couple of things in there so I end up only testing one variable.
And maybe, hopefully, some things will go right on the sequencing side and I’ll be able to annotate my phage’s genome…