This text is based on a set of not es produced for courses given for gradu- ate students in mathematics, computer science and biochemistry during the academic year 1998-1999 at the University of Turku in Turku and at the Royal Institute of Technology (KTH) in Stockholm. The course in Turku was organized by Professor Mats Gyllenberg's groupl and was also included 2 within the postgraduate program ComBi, a Graduate School in Compu- tational Biology,...