The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
A taxonomy of suffix array construction algorithms
Abstract
In 1990, Manber and Myers proposed suffix arrays as a space-saving alternative to suffix trees and described the first algorithms for suffix array construction and use. Since that time, and especially in the last few years, suffix array construction algorithms have proliferated in bewildering abundance. This survey paper attempts to provide simple high-level descriptions of these numerous algorithms that highlight both their distinctive features and their commonalities, while avoiding as much as possible the complexities of implementation details. New hybrid algorithms are also described. We provide comparisons of the algorithms' worst-case time complexity and use of additional space, together with results of recent experimental test runs on many of their implementations.
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Citations
Cites
A Block-sorting Lossless Data Compression Algorithm
Burrows, M. T., & Wheeler, D. J. (1994) · Cited by 2,333
Suffix Arrays: A New Method for On-Line String Searches
Manber, U., & Myers, G. (1993) · SIAM Journal on Computing · doi:10.1137/0222058 · Cited by 1,915
Navarro, G., & Mäkinen, V. (2007) · ACM Computing Surveys · doi:10.1145/1216370.1216372 · Cited by 735
Replacing suffix trees with enhanced suffix arrays
Abouelhoda, M. I., Kurtz, S., & Ohlebusch, E. (2004) · Journal of Discrete Algorithms · doi:10.1016/s1570-8667(03)00065-0 · Cited by 668
Linear work suffix array construction
Kärkkäinen, J., Sanders, P., & Burkhardt, S. (2006) · Journal of the ACM · doi:10.1145/1217856.1217858 · Cited by 433
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
Grossi, R., & Vitter, J. S. (2005) · SIAM Journal on Computing · doi:10.1137/s0097539702402354 · Cited by 431
Simple Linear Work Suffix Array Construction
Kärkkäinen, J., & Sanders, P. (2003) · Lecture Notes in Computer Science · doi:10.1007/3-540-45061-0_73 · Cited by 404
Reducing the space requirement of suffix trees
Kurtz, S. (1999) · Software: Practice and Experience · doi:10.1002/(sici)1097-024x(199911)29:13<1149::aid-spe274>3.0.co;2-o · Cited by 334
The string B-tree: a new data structure for string search in external memory and its applications
Ferragina, P., & Grossi, R. (1999) · Journal of the ACM · doi:10.1145/301970.301973 · Cited by 317
The Myriad Virtues of Subword Trees
Apostolico, A. (1985) · Combinatorial Algorithms on Words · doi:10.1007/978-3-642-82456-2_6 · Cited by 274
Cited by
Adaptive seeds tame genomic sequence comparison
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,281
Ligra: a lightweight graph processing framework for shared memory
Shun, J., & Blelloch, G. E. (2013) · Proceedings of the 18th ACM SIGPLAN symposium on Principles and practice of parallel programming · doi:10.1145/2442516.2442530 · Cited by 798
Navarro, G., & Mäkinen, V. (2007) · ACM Computing Surveys · doi:10.1145/1216370.1216372 · Cited by 735
Indexing Graphs for Path Queries with Applications in Genome Research
Siren, J., Valimaki, N., & Makinen, V. (2014) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2013.2297101 · Cited by 324
Metadata
- Authors
- Puglisi, S. J., Smyth, W. F., & Turpin, A. H.
- Venue
- ACM Computing Surveys
- Published
- 2007-07-06
- Volume
- 39
- Issue
- 2
- Pages
- 4
- ISSN
- 0360-0300 (ISSN-L)
- 1557-7341
- OpenAlex
- W1599214081
- Cited by
- 312
- References
- 23
- FWCI
- 30.73
- Type
- journal article
- Language
- en
- Open access
- closed
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
