Comparative Genomics

What I learned this week #1:

Another week has transpired at my new job as a researcher at TTU and I am being inundated with all sorts of new information. For one thing, I have folks milling around behind my workstation doing all sorts of laboratory things, freezing things in liquid nitrogen (or something else very cold that billows smoke), pipetting (if that is even a word), etc. I’m just disappointed they they’re not wearing lab coats with a mad scientist look in their eye. Unfortunately, my job is much less exotic-looking. I sit in front of a computer, all day long. I do have a pretty fancy set up with two 19-in LCD monitors plugged into a pretty hefty computer (two dual-core processors, 4 GB memory).

I have a number of different projects but they all seem to start in the same place and due to my lack of experience with the biology, I don’t have a good feel with how to follow these initial steps. In essence, the geneticist I work for has a great deal of data collected about the expression of genes in cotton over various varieties of cotton and various developmental phases. So, I start with a list of genes that have been identified to have a particular function in another plant, the most common being Arabidopsis since its genome has been entirely sequenced. We then identify if these genes are present in cotton. Once we have this list of genes we then examine their developmental expression and draw conclusions about their role in cotton.

You know, when I state it like that it seems very simple but there are several steps in each of the above steps that can lead to a great deal of work. So far, I have very little to say about the conclusions we draw. So far, all I have really done is the first phase of identifying these genes in Arabidopsis and begin to compile the list of these genes in cotton. Next week, I’ll begin collected the expression data for some of these genes of particular interest.

I should mention that the first project is actually slightly modified, in that we looked at genes that had specific roles identified first in cotton and then found whether these same genes played similar roles in other species. If any computational biologists, functional geneticists (is that a term?), or bioinformaticists read this and it seems naive, please be kind a realize that I don’t speak the language very well yet. I’m absorbing as much as I can as fast as I can. Having a background in applied mathematics and numerical analysis helps but I still feel handicapped.

Technologically speaking,

  • I learned how to migrate a MSSQL database website to a new server.
  • I learned how to update data in a MySQL database with a pre-built utility website (first time using the “DELETE”, “SELECT” commands with a “LIKE” modifier)
  • I installed PHP and MySQL to run on Microsoft IIS, followed by installing ActiveCollab for project management
  • I used query design mode extensive in Microsoft Access and eventually resorting to SQL statements for “UNION” queries
  • I updated the blast database used by NCBI wwwblast on a local utilities site

4 thoughts on “Comparative Genomics

  1. I love running dual monitors. I use dual 24″ in portrait mode. People just don’t understand how wonderful multiple monitors are until they’ve had a chance to try them out. If you want to run your dual displays from your laptop then I personally recommend the CinePort from CineMassive Displays:

    Works wonderfully. You could run up to 4 additional 24″ panels with that guy,


  2. Ooooh…multiple monitors *and* liquid nitrogen. Paul would be in heaven. At his previous job, there was a vat of liquid nitrogen that was used supposed to be used to test the computer chips at extreme freezing temperatures. I think it was used as much for freezing potato chips and other assorted things as often as it was used for the computer chips.

    I hope you really enjoy this position–it sounds interesting even if I understand about 1/1000th of what you’re actually doing (and that part is probably wrong).


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