By Matthew Williams
I am not the biggest fan of genome annotation. It’s not that I don’t find genetics interesting; although I know little about genetics, I find the topic fascinating. The problem lies within the cut and dry process of annotating.
For starters, I had to download Virtual Box because the programs only work on Windows, and I own a Mac. The interface on Virtual Box is just poor. The screen that I can work on in Virtual box is about 1/4 of my entire computer screen. There might be a way to better this situation, but I am not the best with technology, so it is frustrating for me.
Next, I find the annotation process repetitive and boring. I was never able to blast the entire genome, so I have to copy and paste the amino acid sequence for each gene and personally blast them using the blastp website. It just gets old after awhile. It would be nice if I could just copy and paste the results into DNA Master, but of course it doesn’t work that way. That would just make too much sense.
To continue, I don’t understand how HHPred can predict the function of a gene. My understanding is that the program compares the amino acid sequence of a gene to a bunch of databases and magically can predict the folds in the protein, and as a result determines its function. To HHPred’s credit, I do not understand a lot about genetics or how folds work in proteins. But all I am saying is that if I understood how it worked, the annotation process would be more enticing…. Maybe…
Yes, the source of most of my complaining lies in my own incompetence. I do want to learn more about genetics, and I will do so when I have free time. I could probably fit it in my free time in between my two-a-day training sessions for soccer, 16 credit course load, or my 15 hours worth of research I do every week.
But in all seriousness, I do have a problem with the annotation process. It seems like whenever we come across something new or different, we are supposed to change it to be similar to the other genomes that have been annotated. For example “TTG start sites are less common.” Well if everyone annotating a genome has this mentality and therefore changes the start site to fit the mold, then of course TTG start sites are going to be less common. Also predicting the function of genes based on earlier annotations seems sketchy. While the people who developed the DNA Master Annotation Guide have way more experience and knowledge about genetics and annotation than I do, I would like to pose a question for them. Does their “guidelines for annotation” foster the potential for diversity in phage genomes?
To conclude, I miss the wet lab. I want to develop an experiment to quantify the diffusion rate of Phatniss. I am having some trouble developing a protocol to do so, but I thought it would be cool to compare the difference of diffusion rates in different densities of agar. In a practical sense, this would relate to the diffusion rate in different densities of soil.