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The motivation for this effort was the observation that, while describing and recognizing patterns in sequence data is a key task in biology, this has mainly been done with tools of limited expressive power, such as regular expression search programs, and without regard to well-understood formal underpinnings of computational linguistics. In attempting to characterize the range of phenomena that need to be captured in biological sequences, it was discovered that the tools and techniques of formal language theory offered surprising insights into the structure and behavior of these molecules. After introducing the very simple mathematical foundations for these investigations, this article will review three major lines of research. These can largely be found in more fully developed form in referenced publications, though some new material is also included in each case. 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