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This article is part of the supplement: Proceedings of the 2012 International Conference on Intelligent Computing (ICIC 2012)

Open Access Proceedings

Locating tandem repeats in weighted sequences in proteins

Hui Zhang1, Qing Guo2* and Costas S Iliopoulos3

Author affiliations

1 College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China

2 Corresponding author. College of Computer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China

3 Department of Computer Science, King's College London Strand, London WC2R 2LS, England

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Citation and License

BMC Bioinformatics 2013, 14(Suppl 8):S2  doi:10.1186/1471-2105-14-S8-S2

Published: 9 May 2013


A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to locate all the tandem repeats in a weighted sequence. A repeated substring is called a tandem repeat if each occurrence of the substring is directly adjacent to each other. By introducing the idea of equivalence classes in weighted sequences, we identify the tandem repeats of every possible length using an iterative partitioning technique. We also present the algorithm for recording the tandem repeats, and prove that the problem can be solved in O(n2) time.