Transforming a set of biological flat file librariesto a fast access network

Abstract

SRS (Sequence Retrieval System), an indexing system for flat file libraries, provides fast access to individual library entries via retrie by keywords from rious data fields. SRS is now also able to build indices using cross–references that most libraries provide. Fifteen libraries of DNA and protein sequences and structures have been selected. These libraries interact with at least one other by means of cross–references. Indexing these cross–references allows a complete network of libraries to be built. In the network an entry from one library can be linked in principle to every other library. If two libraries are not directly cross–referenced, the linkage can be made with a succession of single links between neighbouring, cross–referenced libraries. A new operator has been added to the query language of SRS for convenient specification of links amongst complete libraries or entry sets generated by previous queries on particular libraries. All the information in the network can now be used to retrieve an entry in a specific library, e.g. the full information given in amino acid sequence entries from SwissProt can now be used to retrieve related tertiary structure entries from PDB. Furthermore, a search in a single library can be extended to a search in the complete library network, e.g. all entries in all databases pertaining to elastase can be found.