String matching with swaps in a weighted sequence

Authors:
Hui Zhang;Qing Guo;Costas S. Iliopoulos
Affiliations:
Department of Computer Science, King's College London Strand, London, England;Department of Computer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China;Department of Computer Science, King's College London Strand, London, England
Venue:
CIS'04 Proceedings of the First international conference on Computational and Information Science
Year:
2004

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Abstract

A weighted sequence is a string where a set of characters may appear in certain positions with respectively known probabilities of occurrence. We concentrate on the problem of pattern matching with swaps (swapped matching) in a weighted sequence, that is to locate all the positions in the sequence where there exists a swapped match of the pattern that has probability of appearance greater than a predefined constant. In this case, the number of swaps is not limited. We present a method for reducing the problem of swapped matching in a weighted sequence to the problem in a set of maximal factors of the sequence. We then give a almost optimal solution that takes O(nlogmlogσ) time.