A unified approach to word occurrence probabilities
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Re-describing an algorithm by Hopcroft
Theoretical Computer Science
Automata and Computability
Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences
Introduction To Automata Theory, Languages, And Computation
Introduction To Automata Theory, Languages, And Computation
Theory of Codes
Theoretical Computer Science
Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Five Determinisation Algorithms
CIAA '08 Proceedings of the 13th international conference on Implementation and Applications of Automata
Efficient exact motif discovery
Bioinformatics
Finite automata and their decision problems
IBM Journal of Research and Development
Probabilistic Arithmetic Automata and Their Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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 pattern popular in bioinformatics, namely (sets of) generalized strings and (generalized) strings with a Hamming neighborhood.