A protein sequence database cross-field association system

The authors approach the problem of obtaining the best query to select an arbitrarily given subset of a database. In particular, they are interested in automatically obtaining the best description for the function of a given protein sequence pattern. It is assumed that such a description is the query on the functional annotation of a protein sequence database having the closest extension in the database to the extension of the pattern. The implementation of an algorithm is presented for efficiently searching the query space when negation is not considered, and a method is developed in which such an implementation is used to search exhaustively a protein sequence database for biologically relevant protein sequence patterns.