Abstract
The suffix tree of string w is a text indexing structure that represents all suffixes of w. A sparse suffix tree of w represents only a subset of suffixes of w. An application to sparse suffix trees is composite pattern discovery from biological sequences. In this paper, we introduce a new data structure named sparse directed acyclic word graphs (SDAWGs), which are a sparse text indexing version of directed acyclic word graphs (DAWGs) of Blumer et al. We show that the size of SDAWGs is linear in the length of w, and present an on-line linear-time construction algorithm for SDAWGs.
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
Weiner, P.: Linear pattern-matching algorithms. In: Proc. of 14th IEEE Ann. Symp. on Switching and Automata Theory, pp. 1–11 (1973)
Crochemore, M., Rytter, W.: Jewels of Stringology. World Scientific, Singapore (2002)
Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Cambridge (1997)
Kärkkänen, J., Ukkonen, E.: Sparse suffix trees. In: Cai, J.-Y., Wong, C.K. (eds.) COCOON 1996. LNCS, vol. 1090, pp. 219–230. Springer, Heidelberg (1996)
Inenaga, S., Kivioja, T., Mäkinen, V.: Finding missing patterns. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 463–474. Springer, Heidelberg (2004)
Bannai, H., Hyyrö, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S.: An O(N 2) algorithm for discovering optimal boolean pattern pairs. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1, 159–170 (2004)
Inenaga, S., Bannai, H., Hyyrö, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S.: Finding optimal pairs of cooperative and competing patterns with bounded distance. In: Suzuki, E., Arikawa, S. (eds.) DS 2004. LNCS (LNAI), vol. 3245, pp. 32–46. Springer, Heidelberg (2004)
Baeza-Yates, R., Gonnet, G.H.: Efficient text searching of regular expressions. In: Ronchi Della Rocca, S., Ausiello, G., Dezani-Ciancaglini, M. (eds.) ICALP 1989. LNCS, vol. 372, pp. 46–62. Springer, Heidelberg (1989)
Andersson, A., Larsson, N.J., Swanson, K.: Suffix trees on words. Algorithmica 23, 246–260 (1999)
Inenaga, S., Takeda, M.: On-line linear-time construction of word suffix trees. In: Lewenstein, M., Valiente, G. (eds.) CPM 2006. LNCS, vol. 4009, pp. 60–71. Springer, Heidelberg (2006)
Blumer, A., Blumer, J., Haussler, D., Ehrenfeucht, A., Chen, M.T., Seiferas, J.: The smallest automaton recognizing the subwords of a text. Theoretical Computer Science 40, 31–55 (1985)
Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14, 249–260 (1995)
Blumer, A., Blumer, J., Haussler, D., McConnell, R., Ehrenfeucht, A.: Complete inverted files for efficient text retrieval and analysis. Journal of the ACM 34, 578–595 (1987)
Inenaga, S., Hoshino, H., Shinohara, A., Takeda, M., Arikawa, S., Mauri, G., Pavesi, G.: On-line construction of compact directed acyclic word graphs. Discrete Applied Mathematics 146, 156–179 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Inenaga, S., Takeda, M. (2006). Sparse Directed Acyclic Word Graphs. In: Crestani, F., Ferragina, P., Sanderson, M. (eds) String Processing and Information Retrieval. SPIRE 2006. Lecture Notes in Computer Science, vol 4209. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880561_6
Download citation
DOI: https://doi.org/10.1007/11880561_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-45774-9
Online ISBN: 978-3-540-45775-6
eBook Packages: Computer ScienceComputer Science (R0)