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Minimum Unique Substrings and Maximum Repeats

Ilie L., Smyth W.F.

Fundamenta Informaticae

2011

Vol. 110, nr 1-4

183-195

Unique substrings appear scattered in the stringology literature and have important applications in bioinformatics. In this paper we initiate a study of minimum unique substrings in a given string; that is, substrings that occur exactly once while all their substrings are repeats. We discover a strong duality between minimum unique substrings and maximum repeats which, in particular, allows fast computation of one from the other. We give several optimal algorithms, some of which are very simple and efficient. Their combinatorial properties are investigated and a number of open problems are proposed.