Molecular biology is becoming a major source of new open problems for theoretical computer science. This research identifies emerging combinatorial problems in genome rearrangements and DNA physical mapping and to solve open biological problems using combinatorial techniques. In particular, this work develops algorithms for the open biological problem of constructing evolutionary scenarios of genome rearrangements in herpes viruses. In considering possible vaccine strategies for human herpes viruses, systematic knowledge of their genetic capabilities will be invaluable.
