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(n 2) time.
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References
Brodal, G.S., Lyngsø, R.B., Pedersen, C.N.S., Stoye, J.: Finding Maximal Pairs with Bounded Gap. Journal of Discrete Algorithms, Special Issue of Matching Patterns 1(1), 77–104 (2000)
Christodoulakis, M., Iliopoulos, C.S., Mouchard, L., Perdikuri, K., Tsakalidis, A., Tsichlas, K.: Computation of repetitions and regularities on biological weighted sequences. Journal of Computational Biology 13(6), 1214–1231 (2006)
Christodoulakis, M., Iliopoulos, C.S., Perdikuri, K., Tsichlas, K.: Searching the regularities in weighted sequences. In: Proc. of the International Conference of Computational Methods in Science and Engineering. Lecture Series on Computer and Computational Sciences, pp. 701–704. Springer, Heidelberg (2004)
Crochemore, M.: An Optimal Algorithm for Computing the Repetitions in a Word. Information Processing Letter 12(5), 244–250 (1981)
Franêk, F., Smyth, W.F., Tang, Y.: Computing All Repeats Using Suffix Arrays. Journal of Automata, Languages and Combinatorics 8(4), 579–591 (2003)
Guo, Q., Zhang, H., Iliopoulos, C.S.: Computing the λ-covers of a string. Information Sciences 177(19), 3957–3967 (2007)
Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)
Iliopoulos, C.S., Makris, C., Panagis, Y., Perdikuri, K., Theodoridis, E., Tsakalidis, A.: Efficient Algorithms for Handling Molecular Weighted Sequences. IFIP Theoretical Computer Science 147, 265–278 (2004)
Iliopoulos, C.S., Moore, D.W.G., Park, K.: Covering a String. Algorithmica 16, 288–297 (1996)
Iliopoulos, C.S., Mouchard, L., Perdikuri, K., Tsakalidis, A.: Computing the repetitions in a weighted sequence. In: Proc. of the 8th Prague Stringology Conference (PSC 2003), pp. 91–98 (2003)
Iliopoulos, C.S., Perdikuri, K., Zhang, H.: Computing the regularities in biological weighted sequence. In: String Algorithmics. NATO Book series, pp. 109–128 (2004)
Li, Y., Smyth, W.F.: Computing the Cover Array in Linear Time. Algorithmica 32(1), 95–106 (2002)
Ohno, S.: Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes. Journal of Molecular Evolution 20, 313–321 (1984)
Zhang, H., Guo, Q., Iliopoulos, C.S.: Algorithms for Computing the λ-regularities in Strings. Fundamenta Informaticae 84, 33–49 (2008)
Zhang, H., Guo, Q., Iliopoulos, C.S.: Loose and strict repeats in weighted sequences. In: Proc. of the International Conference on Intelligent Computing, ICIC 2009 (accepted 2009)
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Zhang, H., Guo, Q., Iliopoulos, C.S. (2010). Varieties of Regularities in Weighted Sequences. In: Chen, B. (eds) Algorithmic Aspects in Information and Management. AAIM 2010. Lecture Notes in Computer Science, vol 6124. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14355-7_28
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DOI: https://doi.org/10.1007/978-3-642-14355-7_28
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