Construction of minimal DFAs from biological motifs

Details Construction of minimal DFAs from biological motifs Construction of minimal DFAs from biological motifs

2010-04-08

arxiv.org/abs/1004.1298v2

Computer Science

Formal Languages and Automata Theory

Scientific paper

Deterministic finite automata (DFAs) are constructed for various purposes in computational biology. Little attention, however, has been given to the efficient construction of minimal DFAs. In this article, we define simple non-deterministic finite automata (NFAs) and prove that the standard subset construction transforms NFAs of this type into minimal DFAs. Furthermore, we show how simple NFAs can be constructed from two types of patterns popular in bioinformatics, namely (sets of) generalized strings and (generalized) strings with a Hamming neighborhood.

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