This week I spent a considerable amount of time trying to get gnuplot to work. Unfortunately, it does not seem to work well with Mac OS X no matter how many ways you try to install it. From now on I think I'll just go to the lab to produce my graphs. However, I will continue to try to get gnuplot to work.
One of my other goals this week was to alter the experiments I have been running. Because the sequences tend to get stuck at one kmer frequency score for a large number of trials, Dr. Papamichail suggested "breaking" the kmers by doing localized random synonymous changes in order to force the score to change. For the most part the function itself seems to be working but it is still producing some of the error messages I built into it. Currently I'm working on identifying what cases are causing those error messages to appear and how I can adjust my method to accommodate them. Once I have fixed that issue I'll run trials of 1000 this time instead of trials of 100 and will also play around with longer k-mer lengths. Once I have some data I will experiment with gnuplot to see what type of graph will give the best representation of the data.
One of my other goals this week was to alter the experiments I have been running. Because the sequences tend to get stuck at one kmer frequency score for a large number of trials, Dr. Papamichail suggested "breaking" the kmers by doing localized random synonymous changes in order to force the score to change. For the most part the function itself seems to be working but it is still producing some of the error messages I built into it. Currently I'm working on identifying what cases are causing those error messages to appear and how I can adjust my method to accommodate them. Once I have fixed that issue I'll run trials of 1000 this time instead of trials of 100 and will also play around with longer k-mer lengths. Once I have some data I will experiment with gnuplot to see what type of graph will give the best representation of the data.