Methods for Global Organization of All Known Protein Sequences It Was a Pleasure to Work with the Great Team of Students with Whom I Created the Protomap Web Site. I Thank

Acknowledgments First, I would like to thank my advisors: Nati Linial and Tali Tishby of the computer science department and Michal Linial of the life science department at the Hebrew University. Within the last ve years we have come a long way together, and I'm grateful for their guidance, support, warmth and generous help all these years. I would like to thank my colleagues and friends in the machine learning lab, with whom I spent most of the last ve years: for all their help and for being great company. A special thanks to Ran El-Yaniv, a dear friend who encouraged me to keep believing in myself. I very much enjoyed working with Gill Bejerano, with whom I am still working on fascinating new directions. I would next like to thank all of my colleagues and friends in the molecular genetics and biotechnology lab headed for the great time I had every Thursday in our journal club group meetings. Besides the many papers I had in my bag after each such meeting, it was also great fun. A very special thanks to Yael Altuvia for her continuous and wonderful help and support, and to Hanah Margalit, who was like an advisor for me, always happy to answer questions and give advice, as well as give me encouragement in hard times. I thank Amnon Barak for making the MOSIX parallel system available, and the people in Compugen Ltd. who gave me access to their Bioccelerator and to their software. Ran El-Yaniv for critically reading parts of this manuscript and for making many helpful comments, and Avner Magen for valuable suggestions. A special thanks to Nati Linial, my advisor, who with much patience read most of this thesis, commenting, correcting my English, and improving my writing style. To my family, especially my mother and father for their tremendous love and encouragement, and for continually reminding me that they will be happy with whatever I choose to do (always leaving me the option of becoming a carpenter). And last, to my best friends, Yoram Gdalyahu and Rami Doron, for their enormous help and for their invaluable friendship during these intensive years.