Alphabet-independent linear-time construction of compressed suffix arrays using o (n log n)-bit working space

Theoretical Computer Science

Volumn 385, Issue 1-3, 2007, Pages 127-136

  Na, Joong Chae ^a   Park, Kunsoo ^b  

^a Konkuk University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Burrows Wheeler transform; Compressed suffix array; FM index; Index data structure

Indexed keywords

ALGORITHMS; DATA STRUCTURES; TECHNICAL PRESENTATIONS;

BURROWS-WHEELER TRANSFORMS; COMPRESSED SUFFIX ARRAYS; INDEX DATA STRUCTURES;

BIOINFORMATICS;

EID: 34548697512     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2007.05.030     Document Type: Article

References (18)

1. M. Burrows, D.J. Wheeler, A block-sorting lossless data compression algorithm, Technical Report 124, Digital Equipment Corporation, Paolo Alto, California, 1994
2. D.R. Clark, Compact pat trees, Ph.D. Thesis, University of Waterloo, Waterloo, 1996
3. M. Farach, Optimal suffix tree construction with large alphabets, in: Proceedings of the 38th Annual IEEE Symposium on Foundations of Computer Science, 1997, pp. 137-143
4. Farach-Colton M., Ferragina P., and Muthukrishnan S. On the sorting-complexity of suffix tree construction. Journal of the ACM 47 6 (2000) 987-1011
5. Ferragina P., and Manzini G. Indexing compressed text. Journal of the ACM 52 4 (2005) 552-581
6. Gonnet G.H., Baeza-Yates R., and Snider T. New indices for text: Pat trees and pat arrays. In: Frakes W.B., and Baeza-Yates R. (Eds). Information Retrieval: Data Structures & Algorithms (1992), Prentice Hall 66-82
7. Grossi R., and Vitter J.S. Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM Journal on Computing 35 2 (2005) 378-407
8. D. Gusfield, An "Increment-by-one" approach to suffix arrays and trees, 1990, Manuscript
9. W.K. Hon, T.W. Lam, K. Sadakane, W.K. Sung, Constructing compressed suffix arrays with large alphabets, in: Proceedings of the 14th International Symposium on Algorithms and Computation, 2003, pp. 240-249
10. Hon W.K., Lam T.W., Sadakane K., Sung W.K., and Yiu S.M. A space and time efficient algorithm for constructing compressed suffix arrays. Algorithmica (2007) 10.1007/s00453-006-1228-8
11. W.K. Hon, K. Sadakane, W.K. Sung, Breaking a time-and-space barrier in constructing full-text indices, in: Proceedings of the 44th Annual IEEE Symposium on Foundations of Computer Science, 2003, pp. 251-260
12. Kärkkäinen J., Sanders P., and Burkhardt S. Linear work suffix array construction. Journal of the ACM 53 6 (2006) 918-936
13. Kim D.K., Sim J.S., Park H., and Park K. Constructing suffix arrays in linear time. Journal of Discrete Algorithms 3 2-4 (2005) 126-142
14. Ko P., and Aluru S. Space efficient linear time construction of suffix arrays. Journal of Discrete Algorithms 3 2-4 (2005) 143-156
15. T.W. Lam, K. Sadakane, W.K. Sung, S.M. Yiu, A space and time efficient algorithm for constructing compressed suffix arrays, in: Proceedings of the 9th International Computing and Combinatorics Conference, 2002, pp. 401-410
16. Manber U., and Myers G. Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22 5 (1993) 935-948
17. J.I. Munro, Tables, in: Proceedings of Conference on Foundations of Software Technology and Theoretical Computer Science, 1996, pp. 37-42
18. Sadakane K. New text indexing functionalities of the compressed suffix arrays. Journal of Algorithms 48 2 (2003) 294-313