Tough Choices

By Derek MacMath

We are now at the midpoint of our spring semester here at Hopkins, and the time has come to make some touch choices.  Tough choices about how to finish the first half of the class, and tough choices about what to do for the rest.

Once we all got the hang of annotating genes, the first half of Manatee’s genome annotation was a breeze.  Despite some of the disagreements between GeneMark and Glimmer that Norah mentioned in her post, the annotating went well.  Now that we are at the back end of Manatee’s genome, being certain about genes is getting harder.  For example, there are some possible genes that the computer programs called, and even though they seem legitimate at first, they are less than 80 base pairs long.  There are other cases in which the gene seems legitimate but it completely lacks coding potential, or there are large gaps (200+ base pairs) and neither GeneMark nor Glimmer called a gene.  This is where our touch decisions come in.   Do we call these genes, or not?

These tough decisions cannot be made easily, and that is where the second half of the semester comes in.  After spring break, we will each present a proposal for a special project, so over the next week we will all have to decide how to spend the rest of the semester.  These projects can either be lab based or computer based.  Although lab work is fun, a computer based special project could result in some useful insight about these questionable genes.  Using Phamerator, it is possible to investigate specific DNA sequences, see how common they are, and find out where they appear in other A1 subcluster phage.  Even though DNA master is great, it can be a bit hard to navigate and it was always a pain synthesizing data from multiple databases into one.  Perhaps a good special project could be mapping out Manatee’s genome in a way that makes it easy to compare to other A1 phage.  But then again, I miss the lab.

So during the next week, I’ll be making a tough choice.

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