Finite Query Languages for Sequence Databases

This paper develops a query language for sequence databases, such as genome databases and text databases. Unlike relational data, queries over sequential data can easily produce infinite answer sets, since the universe of sequences is infinite, even for a finite alphabet. The challenge is to develop query languages that are both highly expressive and finite. This paper develops such a language. It is a subset of a recently developed logic called Sequence Datalog [19]. Sequence Datalog distinguishes syntactically between subsequence extraction and sequence construction. Extraction creates sequences of bounded length, and leads to safe recursion; while construction can create sequences of arbitrary length, and leads to unsafe recursion. In this paper, we develop syntactic restrictions for Sequence Datalog that allow sequence construction but preserve finiteness. The main idea is to use safe recursion to control and limit unsafe recursion. The main results are the definition of a finite form of recursion, called domain bounded recursion, and a characterization of its complexity and expressive power. Although finite, the resulting class of programs is highly expressive, since its data complexity is complete for the elementary functions.