Computational Complexity of Word Counting

Authors:
Mireille Régnier
Affiliations:
-
Venue:
JOBIM '00 Selected papers from the First International Conference on Computational Biology, Biology, Informatics, and Mathematics
Year:
2000

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Abstract

Evaluation of the frequency of occurrences of a given set of patterns in a DNA sequence has numerous applications and has been extensively studied recently. We discuss the computational complexity for explicit formulae derived by several authors. We introduce a correlation automaton, that minimizes this complexity. This is crucial for practical applications. Notably, it allows to deal with the Markovian probability model. The case of patterns with some unspecified characters - approximate searching, regular expressions, ... - is addressed.