RNA Secondary Structure Prediction

Sophie Schneiderbauer

For my Bachelor Thesis in the domain of Bioinformatics, I decided to work in the field of secondary structure prediction of RNA. I have made a program which develops good predictions for a given RNA sequence, by using a dynamic algorithm. The user of the program can choose between three different methods to make the prediction: Either he or she can use the Nussinov-algorithm, the Zuker-algorithm or the Zuker-algorithm with one or two pseudoknots. Later on, I will provide more specific information about these different methods.
First of all, I am going to give a rough sketch of the background in the area of genetic biology. I am going to explain what RNA is, where it is used and why it is important to predict its secondary structure. Therewith will be explained the differences between the different structures and in more detail the existing forms of secondary structure elements.
In the next section an overview of several prediction methods will be given and the methods I have used in my program will be explained precisely.
Furthermore, an outline of the program and its structure will be given. I am going to illustrate how it can be used and how the algorithms and the graphical representations have been implemented.
Afterwards, I am going to explain briefly how I varied the values for the parameters, how the accuracy has been measured and what the results have been.
At the end of this thesis, the program will be compared to other, already existing programs and finally I am going to evaluate the program critically.