Annotating genes before Spring Break!

By Annette Wang

Phage Hunting this semester has been an interesting change from the fall. We haven’t been in the lab and instead we’ve been sitting in a classroom annotating genes. Doesn’t sound as fun, but it’s been an obstacle course that’s turned out pretty cool.

After successfully downloading all the software and setting up Windows on Mac (why can’t there be a Mac version of DNAmaster???) we began the process of annotating genes. Our first gene took as us an entire hour, as we had trouble figuring out how the coding potential graphs worked, how to use HHpred, and the BLAST just WOULDN’T BLAST. But after working through a few genes we got a better grasp of what was going on. I think our second one took us half an hour, and by the fifth one it took us ten minutes.

Annotating genes has been an interesting skill to learn. I don’t think I’ve quite mastered it yet. Last class my group determined all the gaps between our assigned genes wrong because we didn’t understand how to determine gaps for reverse genes. In the end we figured out that in order to determine the gap for a reverse gene, you have to look at the 5’ end of the next gene, compare it to the 3’ end of the previous gene in order to get the gap for the previous gene. We’ve had trouble annotating the genes fifty and onwards as they’re kind of iffy, but when you actually get what’s going on and what each category your annotating for means, it’s pretty cool.

We’re going to start using Phamerator after Spring Break and I’m really curious to what we can get out of it – after all, it did take so much effort to get on our Macs! After that, we’ll be back in the lab working on our projects. I’m definitely excited for that! Have a great Spring Break everyone!

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