Abstract
Approximate searching using an index is an important application in many fields. In this paper we introduce a new data structure called the gapped suffix array for approximate searching in the Hamming distance model. Building on the well known filtration approach for approximate searching, the use of the gapped suffix array can improve search speed by avoiding the merging of position lists.
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
Böckenhauer, H.-J., Bongartz, D.: Algorithmic Aspects of Bioinformatics. Springer, Heidelberg (2007)
Crochemore, M., Hancart, C., Lecroq, T.: Algorithms on Strings, 392 p. Cambridge University Press, Cambridge (2007)
Fischer, J., Heun, V.: A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array. In: Chen, B., Paterson, M., Zhang, G. (eds.) ESCAPE 2007. LNCS, vol. 4614, pp. 459–470. Springer, Heidelberg (2007)
Grossi, R., Gupta, A., Vitter, J.S.: High-order entropy-compressed text indexes. In: SODA 2003: Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms, pp. 841–850. Society for Industrial and Applied Mathematics, Philadelphia (2003)
Grossi, R., Vitter, J.S.: Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching. SIAM J. Comput. 35(2), 378–407 (2005)
Gusfield, D.: Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, Cambridge (1997)
Landau, G.M., Vishkin, U.: Efficient string matching with k mismatches. Theor. Comput. Sci. 43, 239–249 (1986)
Landau, G.M., Vishkin, U.: Fast string matching with k differences. J. Comput. Syst. Sci. 37(1), 63–78 (1988)
Navarro, G.: A guided tour to approximate string matching. ACM Comput. Surv. 33(1), 31–88 (2001)
Navarro, G., Baeza-Yates, R.A., Sutinen, E., Tarhio, J.: Indexing methods for approximate string matching. IEEE Data Eng. Bull. 24(4), 19–27 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Crochemore, M., Tischler, G. (2010). The Gapped Suffix Array: A New Index Structure for Fast Approximate Matching. In: Chavez, E., Lonardi, S. (eds) String Processing and Information Retrieval. SPIRE 2010. Lecture Notes in Computer Science, vol 6393. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16321-0_37
Download citation
DOI: https://doi.org/10.1007/978-3-642-16321-0_37
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16320-3
Online ISBN: 978-3-642-16321-0
eBook Packages: Computer ScienceComputer Science (R0)