This paper is an introduction to the programmer's interface of version 1.1 of the FIRE engine. The FIRE engine is a C++ class library implementing finite automata and regular expression algorithms. The algorithms implemented in the toolkit are almost all of those presented in the taxonomies of finite automata algorithms [Wat93a, Wat93b]. None of the implementation details of the library are discussed --- such design and implementation details are given in [Wat94]. The toolkit is unique in providing implementations of all of the known algorithms for constructing finite automata. The implementations, which were developed with efficiency in mind, are intended for use in production quality applications. No shell or graphical user-interface is provided, as the toolkit is intended for integration into applications. The implementations of the algorithms follow directly from the abstract algorithms appearing in [Wat93a, Wat93b]. As such, the toolkit also serves as an educational example of the...

Abstract. In the context of this paper microsatellites (short approximate tandem repeats) refer to consecutive patterns contained in genomic sequences. A new algorithm to detect such microsatellites in DNA is proposed. The algorithm relies on the construction of finite automata originating from the Moore machine paradigm. The proposed finite automata contain “counting states”. The overall algorithm is designed to support user requirements as expressed by the typical geneticist.