Combining Computation with Database Access in Biomolecular Computing

Protein structure analysis is a very important application for database technology, with industrial spinoffs. It is also very demanding because sequence search is so very different from 3-D structure, search. We have developed a common data model for integrating sequence and structure data, and for relating different sequence numbering schemes to 3-D structures. We Lave been able to use our high-level functional language Daplex to express queries of both kinds, but using alternative storage schemas to get good performance in a way that is transparent to the user. Daplex functions can be stored in the database and associated with sub-types in an object-oriented fashion. This architecture allows practising scientists to combine complex geometric calculations with data access, which they need in order to search for complex relationships in the data which may validate or modify their hypotheses.