Computational approaches to discovering semantics in molecular biology

One of the central problems of molecular biology stems from the discovery of the semantics of DNA. This discovery relies in a critical way on a variety of expensive computations. In order to solve these computations, both parallel computers and special-purpose hardware play a major role. The authors discuss the basic methodology involved in discovering the evolutionary structure of both DNA and proteins. Both fundamental issues and implementation issues are considered. The fundamental questions involve determining just how the sequences are to be compared. The implementation issues concern the vast amounts of computation required to execute the known algorithms