Varieties of regularities in weighted sequences

Authors:
Hui Zhang;Qing Guo;Costas S. Iliopoulos
Affiliations:
College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China;College of Computer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China;Department of Computer Science, King's College London Strand, London, England
Venue:
AAIM'10 Proceedings of the 6th international conference on Algorithmic aspects in information and management
Year:
2010

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Abstract

A weighted sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. A common task is to identify repetitive motifs in weighted sequences, with presence probability not less than a given threshold. We consider the problems of finding varieties of regularities in a weighted sequence. Based on the algorithms for computing all the repeats of every length by using an iterative partitioning technique, we also tackle the all-covers problem and all-seeds problem. Both problems can be solved in O(n2) time.