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 sequential data can easily produce in nite answer sets, since the universe of sequences is in nite, even for a nite alphabet. The challenge is to develop query languages that are both highly expressive and nite. This paper develops such a language as a subset of a logic for string databases called Sequence Datalog. The main idea is to use safe recursion to control and limit unsafe recursion. The main results are the de nition of a nite form of recursion, called domain{bounded recursion, and a characterization of its complexity and expressive power. Although nite, the resulting class of programs is highly expressive, since its data complexity is complete for the elementary functions.