There is a lot of similarity between mice and men, but if we would simply put the DNA sequence of mouse and human next to each other they would not look very similar as they would get "out of sync". Where one of the species has additional DNA, we have to offset the other sequence to see new regions of continued similarity. Comparing features across different organisms thus requires such a complex mapping to be taken into consideration.
A masters task on this topic was written by Eivind Gard Lund from 2010 to april 2011. A Python-based framework was developed that used array programming methods (numpy-based) to analyze relations between DNA data sets across organisms. A second master task on the topic was written by Torkil Vederhus from 2012 to april 2013. Here, a Python-based analysis methodology was developed that can detect systematic differences between individuals of the same species.
The goal of the task is to further develop the methodology and implementation of the previous tasks to a level where it can be offered to biologists as an internationally preferred tool for analyzing properties of genomes across organisms or across individuals of the same organism. This could be achieved by building generic components that can be combined in many ways to allow a broad range of precise questions to be asked through a simple interface. Furthermore, it is important to precisely define a model of e.g. distance when we have two genomes that align at several locations. It might be possible to apply developed methodology to ongoing biological research projects at the university.
Students should be skilled in programming and mathematical thinking. No prior knowledge of biology is needed, but an interest for biology could be an advantage.