Abstract
In our previous work, we introduced the concept of semilocal string comparison, and developed for it an efficient method called the seaweed algorithm. In the current paper, we introduce its extension, called the periodic seaweed algorithm. The new algorithm allows efficient exploitation of the periodic structure in one of the input strings. By application of the periodic seaweed algorithm, we obtain new algorithms for the tandem LCS problem and the tandem cyclic alignment problem, improving on existing algorithms in running time.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alves, C.E.R., Cáceres, E.N., Song, S.W.: An all-substrings common subsequence algorithm. Discrete Applied Mathematics 156(7), 1025–1035 (2008)
Benson, G.: Tandem cyclic alignment. Discrete Applied Mathematics 146(2), 124–133 (2005)
Crochemore, M., Landau, G.M., Schieber, B., Ziv-Ukelson, M.: Re-use dynamic programming for sequence alignment: An algorithmic toolkit. In: String Algorithmics. Texts in Algorithmics, vol. 2. College Publications, King’s (2004)
Fischetti, V.A., Landau, G.M., Sellers, P.H., Schmidt, J.P.: Identifying periodic occurrences of a template with applications to protein structure. Information Processing Letters 45(1), 11–18 (1993)
Jackson, B.N., Aluru, S.: Pairwise sequence alignment. In: Handbook of Computational Molecular Biology. Chapman and Hall/CRC Computer and Information Science Series, ch. 1, pp. 1–1 – 1–31. Chapman and Hall/CRC, Boca Raton (2006)
Landau, G.: Can DIST tables be merged in linear time? An open problem. In: Proceedings of the Prague Stringology Conference, p. 1. Czech Technical University in Prague (2006)
Landau, G.M., Myers, E., Ziv-Ukelson, M.: Two algorithms for LCS consecutive suffix alignment. Journal of Computer and System Sciences 73(7), 1095–1117 (2007)
Landau, G.M., Ziv-Ukelson, M.: On the common substring alignment problem. Journal of Algorithms 41(2), 338–359 (2001)
Masek, W.J., Paterson, M.S.: A faster algorithm computing string edit distances. Journal of Computer and System Sciences 20, 18–31 (1980)
Myers, E.W., Miller, W.: Approximate matching of regular expressions. Bulletin of Mathematical Biology 51(1), 5–37 (1989)
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48(3), 443–453 (1970)
Schmidt, J.P.: All highest scoring paths in weighted grid graphs and their application to finding all approximate repeats in strings. SIAM Journal on Computing 27(4), 972–992 (1998)
Sellers, P.H.: The theory and computation of evolutionary distances: Pattern recognition. Journal of Algorithms 1(4), 359–373 (1980)
Tiskin, A.: Semi-local longest common subsequences in subquadratic time. Journal of Discrete Algorithms 6(4), 570–581 (2008)
Tiskin, A.: Semi-local string comparison: Algorithmic techniques and applications. Mathematics in Computer Science 1(4), 571–603 (2008)
Tiskin, A.: Semi-local string comparison: Algorithmic techniques and applications. Technical Report 0707.3619, arXiv (2009)
Wagner, R.A., Fischer, M.J.: The string-to-string correction problem. Journal of the ACM 21(1), 168–173 (1974)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Tiskin, A. (2009). Periodic String Comparison. In: Kucherov, G., Ukkonen, E. (eds) Combinatorial Pattern Matching. CPM 2009. Lecture Notes in Computer Science, vol 5577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02441-2_18
Download citation
DOI: https://doi.org/10.1007/978-3-642-02441-2_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02440-5
Online ISBN: 978-3-642-02441-2
eBook Packages: Computer ScienceComputer Science (R0)