Diploma thesis hIntaRNA - Comparative prediction of sRNA

I herewith affirm that I completed the work myself, and did not use any other than the mentioned sources and utilities. Acknowledgements II Acknowledgements Firstly I would like to thank my parents Gabriele M. König and Anthony D. Wright as well as other family members for their continued support and guidance not only with respect to my work but also with respect to day to day situations. I value your advice. the opportunity to work on this project, and for fruitful discussions on the matter. Furthermore I thank them for giving me the chance to attend the RNA meeting in Kassel. I thank Dr. Jens Georg and Andreas S. Richter for their supervision, patience and the time they invested in me. I am especially thankful to Jens for having the idea behind hIntaRNA in the first place. Furthermore I acknowledge the help of the IT branch of AG Hess for resolving the technical issues I encountered along the way. General gratitude is owed to the entire AG Hess for making every day working easy and enjoyable. I would also like to show my gratitude to Dr. Kai Papenfort who helped me in attaining the only wet lab based result of this thesis. Finally, I thank Matthias Kopf and Beate Kaufmann both of whom have been great friends and colleagues since week one in October 2006. Work would have been much harder without having you guys doing it alongside. Abstract 1 1 Abstract Background: Prediction of targets of bacterial small RNAs (sRNAs) is a very challenging