Abstract
Compact bases formed by motifs called ”irredundant” and capable of generating all other motifs in a sequence have been proposed in [8,10] 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(|Σ|n 2 logn) and O(|Σ|n 2 logn), respectively in [9] and [7], through resort to the FFT-based string searching by Fischer and Paterson [5]. More recently, a solution taking time O(|Σ|n 2) without resort to the FFT was also devised [4].
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Apostolico, A., Tagliacollo, C. (2007). Incremental Discovery of Irredundant Motif Bases in Time O(|Σ|n 2 logn). In: Giancarlo, R., Hannenhalli, S. (eds) Algorithms in Bioinformatics. WABI 2007. Lecture Notes in Computer Science(), vol 4645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74126-8_13
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DOI: https://doi.org/10.1007/978-3-540-74126-8_13
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