Methods for Finding Motifs in Sets of Related Biosequences

Acknowledgements I wish to thank the Norwegian Research Council (NRF) that through grant 100623/410 made it possible for me to do this work. Most of this work has been done in the bioinformatics group at the Department of Informatics, University of Bergen. I have very much enjoyed working in this group, and I wish to thank all group members for providing the nice and inspiring working environment. My main supervisor has been Ingvar Eidhammer, and I wish to thank him for his continuous support and guidance. I also wish to thank Carsten Helgesen, now at the Bergen College, who initially suggested the subject for this thesis. Helgesen has also ooered me help and guidance during my work on this thesis. has introduced me to many of the fascinating problems in bioinformatics. I also wish to thank the people at the Laboratory of Biotechnology, University of Bergen, who have helped me to understand some molecular biology, and in particular Rein Aasland who has helped me, and my co-authors, nding relevant test-cases for the methods presented here. I also wish to thank all the people at the European Bioinformatics Insitute (EBI), where I was lucky to spend half a year in Desmond Higgins' group. Thanks to Higgins for excellent guidance and many interesting discussions, and also to Cedric Notredame for his support and enthusiasm. Thanks also to Alvis Brazma with whom I have had a very fruitful cooperation, and also to Esko Ukkonen, Jaak Vilo, and David Gilbert. Finally I wish to thank my parents and my girl friend Anne Mari for patience and support.