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The application ofcomputational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries tradi- tionally separating genetics, biology, mathematics, physics, and computer science. Com- puters have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function ofgenomes ofhigher organisms, has generated, how- ever, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, be- yond establishing a new kind ofalliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technolo- gies. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with suc- cess. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncer- tainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field.