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Incremental discovery of the irredundant motif bases for all suffixes of a string in O(n2logn) time
2008
Theoretical Computer Science
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(n 2 log n log | Σ |) and O(| Σ | n 2 log 2 n log log n), respectively, using the FFTbased string searching by Fischer and Paterson.
doi:10.1016/j.tcs.2008.08.002
fatcat:wjvrtw4pbrel7epltf3an5xxoi