Comp Bio is complicated

I finished up my first lab rotation two Fridays ago, here at UT Southwestern. It was a pleasant few months with an interesting project, consisting mostly of starting at a computer screen and writing Python scripts, running BLAST searches, and so on. To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this:

There are currently a crap-ton (“crap-ton” is a standard scientific prefix) of bacterial and archaeal genomes published and available on NCBI‘s servers. Archaea, like bacteria, are single-celled prokaryotic organisms. However, they differ from bacteria genomically (and therefore metabolically) in many ways. Some archaeal properties are like those in eukaryotes (like us!), while others are like those in bacteria. So one of the huge unanswered questions in evolution is: how are bacteria, archaea, and eukaryotes related to each other? Or, how would we make a tree of life relating these three domains?

Continue reading

A simple model of selection

Inspired by Dawkins’ METHINKS IT IS LIKE A WEASEL program (hereafter just weasel) described in his book “The Blind Watchmaker,” and wanting to practice my blossoming C++ skills, I decided to write my own version of weasel. It was successful enough, and I found the results interesting enough to warrant discussion. Download the program (Windows .exe file) so you can try it out for yourself (and you can also get the source code if you want). In this post I’ll discuss what the program does and why. In the next post I’ll talk a bit about the results of the program.


Continue reading

Rabies is (are?) neat.

While going through all of my old school stuff from the UofC and uploading it into gmail, I came across the poster project I did for an immuno class at the end of my third (I think) year. It’s saved as a jpeg, so I put it up on flickr for anyone who’s interested in learning how rabies works. It’s pretty impressive how much it can do with so little genome. Anyway, click the image below to learn about rabies!

tRNA pun

I thought of this one day while brushing my teeth. The images make it easier, but this was the original joke:

So one tRNA diffuses up to another and says, “It is frigid in here!” The other tRNA responds, “Well, then go get your codon.”

Read it out loud to get the joke. It isn’t that funny, sadly, but it made me laugh when I thought of it.

The specific tRNA in the image is yeast Phenylalanine tRNA, which I got from RCSB. The number is 1ehz. I used pyMOL to orient and take the images, and then GIMP to add in speech bubbles.