Query languages for sequence databases: Termination and complexity

This paper develops a query language for sequence databases, such as genome databases and text databases. Unlike relational data, queries over sequent ial data can easily produce infinite answer sets since the universe of sequ ences is infinite, even for a finite alphabet. The challenge is to develop query languages that are both highly expressive and finite. This paper deve lops such a language as a subset of a logic for string databases called Seq uence Datalog. 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 r ecursion, called domain-bounded recursion, and a characterization of its co mplexity and expressive power. Although finite, the resulting class of prog rams is highly expressive since its data complexity is complete for the ele mentary functions.