Keys to the Lab!

So I'm finished with trees for the time being. Aside from my PI sending me one every few days as he finishes up his grant stuff and pushes towards publishing, I've been working on a new project.

Unfortunately, it's going to drive me mad.

All those genes I had to annotate on trees? Well, now I'm doing intron analysis. If I hadn't been required to take Intro Genetics, I would have completely forgotten what those were. You see, prokaryotes DON'T have introns, and that's what I've been studying for nearly two years now. In prokaryotes, you find an open reading frame (ORF) and you keep going until you find a stop codon. Nice and neat, no splicing, no guesswork.

Introns are a pain. They can wedge themselves between two amino acids or even within one and you'll be none the wiser until you start translating and realizing that your code is a lot larger than the protein. Hrm. Also, it's impossible to tell an intron from an exon by simply looking at the chromosome or the mRNA.

Cue an awesome little program called DS Gene. I love it already. It gives me potential ORFs; all I have to do is translate them and see if they match the recorded protein structure wherever the genome for these organisms are being held. Most of them are on NCBI, which is just dandy, but there are a few lurking elsewhere in cyberspace, though I think I've tracked most of them down by now.

One little hitch/piece of awesomeness (depending on how you look at it): DS Gene only runs on Windows. I have a Mac, a Mac that stubbornly resists Bootcamp for some reason. So last week I received keys to the lab so I can get in on days that the building is closed (if I need to do so) and run my analysis on the lab computer. Woo!