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The problem of extracting a basis of irredundant motifs from a sequence is considered. In previous work such bases were built incrementally for all suffixes of the input string s in O(n3), where n is the length of s. Faster, non-incremental algorithms have been based on the landmark approach to string searching due to Fischer and Paterson, and exhibit respective time bounds of O(n ...
Compact bases formed by motifs called “irredundant” and capable of generating all other motifs in a sequence have been proposed in recent years and successfully tested in tasks of biosequence analysis and classification. Given a sequence s of n characters drawn from an alphabet Σ, the problem of extracting such a base from s had been previously solved in time O(n2lognlog∣Σ∣) and O(∣Σ∣n2log2nloglogn),...
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