Abstract
A sparse suffix tree is a suffix tree that represents only a subset of the suffixes of the text. This is in contrast to the standard suffix tree that represents all suffixes. By selecting a small enough subset, a sparse suffix tree can be made to fit the available storage, unfortunately at the cost of increased search times. The idea of sparse suffix trees goes back to PATRICIA tries. Evenly spaced sparse suffix trees represent every kth suffix of the text. In the paper, we give general construction and search algorithms for evenly spaced sparse suffix trees, and present their run time analysis, both in the worst and in the average case. The algorithms are further improved by using so-called dual suffix trees.
A work supported by the Academy of Finland.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
References
A. Andersson, N. J. Larsson, and K. Swansson, Suffix trees on words, in Proc. 7th Symposium on Combinatorial Pattern Matching (CPM), 1996. To appear.
A. Andersson and S. Nilsson, Improved behaviour of tries by adaptive branching, Inf. Process. Lett., 46 (1993), pp. 295–300.
-, Efficient implementation of suffix trees, Software—Practice and Experience, 25 (1995), pp. 129–141.
A. Apostolico, The myriad virtues of subword trees, in Combinatorial Algorithms on Words, A. Apostolico and Z. Galil, eds., Springer-Verlag, 1985, pp. 85–95.
A. Apostolico and W. Szpankowski, Self-alignments in words and their applications, Journal of Algorithms, 13 (1992), pp. 446–467.
G. H. Gonnet, R. A. Baeza-Yates, and T. Snider, Lexicographical indices for text: Inverted files vs. Pat trees, Technical Report OED-91-01, Centre for the New OED, University of Waterloo, 1991.
R. W. Irving, Suffix binary search trees, Technical report TR-1995-7, Computing Science Department, University of Glasgow, Apr. 1995.
J. Kärkkäinen, Suffix cactus: A cross between suffix tree and suffix array, in Proc. 6th Symposium on Combinatorial Pattern Matching, CPM 95, 1995, pp. 191–204.
D. E. Knuth, J. H. Morris, and V. R. Pratt, Fast pattern matching in strings, SIAM J. Comput., 6 (1977), pp. 323–350.
S. R. Kosaraju and A. L. Delcher, Large-scale assembly of DNA strings and space-efficient construction of suffix trees, in Proc. 27th Annual ACM Symposium on Theory of Computing (STOC), 1995, pp. 169–177.
U. Manber and G. Myers, Suffix arrays: A new method for on-line string searches, SIAM J. Comput., 22 (1993), pp. 935–948.
U. Manber and S. Wu, A two-level approach to information retrieval, Technical Report TR 93-06, University of Arizona, 1993.
E. M. McCreight, A space-economical suffix tree construction algorithm, J. Assoc. Comput. Mach., 23 (1976), pp. 262–272.
D. R. Morrison, PATRICIA—Practical Algorithm To Retrieve Information Coded in Alphanumeric, J. Assoc. Comput. Mach., 15 (1968), pp. 514–534.
E. Ukkonen, On-line construction of suffix-trees, Algorithmica, 14 (1995), pp. 249–260.
P. Weiner, Linear pattern matching algorithms, in Proc. IEEE 14th Annual Symposium on Switching and Automata Theory, 1973, pp. 1–11.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1996 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kärkkäinen, J., Ukkonen, E. (1996). Sparse suffix trees. In: Cai, JY., Wong, C.K. (eds) Computing and Combinatorics. COCOON 1996. Lecture Notes in Computer Science, vol 1090. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-61332-3_155
Download citation
DOI: https://doi.org/10.1007/3-540-61332-3_155
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-61332-9
Online ISBN: 978-3-540-68461-9
eBook Packages: Springer Book Archive