Monoids? What are they? How are the wild kind different? This monograph examines the wild variety of the free monoid, the mathematical object which underlies the analysis of DNA and RNA sequences containing ambiguous (wild) characters. It includes a study of the famous Knuth-Morris-Pratt string search algorithm, showing why knowledge of the underlying monoid is important, and presenting a linear-time extension which correctly handles strings over wild monoids.
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