Faster suffix sorting

Theoretical Computer Science

Volumn 387, Issue 3, 2007, Pages 258-272

  Larsson, N Jesper ^a   Sadakane, Kunihiko ^b  

^a Apptus Technologies   (Sweden)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

Burrows Wheeler transform; Suffix arrays

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; DATA COMPRESSION; PATTERN MATCHING; ROBUSTNESS (CONTROL SYSTEMS);

BURROWS-WHEELER TRANSFORM; STRING MATCHING; SUFFIX ARRAYS;

SORTING;

EID: 35448995660     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2007.07.017     Document Type: Article

References (31)

1. Bernhard Balkenhol, Stefan Kurtz, Yuri M. Shtarkov, Modifications of the burrows and wheeler data compression algorithm, in: Proceedings of the IEEE Data Compression Conference, 1999, pp. 188-197
2. Bentley J.L., and McIlroy M.D. Engineering a sort function. Software - Practice and Experience 23 11 (1993) 1249-1265
3. Jon L. Bentley, Robert Sedgewick, Fast algorithms for sorting and searching strings, in: Proceedings of the eighth Annual ACM-SIAM Symposium on Discrete Algorithms, 1997, pp. 360-369
4. Burkhardt S., and Kärkkäinen J. Fast lightweight suffix array construction and checking. Proc. CPM. LNCS vol. 2676 (2003) 55-69
5. Michael Burrows, David J. Wheeler, A block-sorting lossless data compression algorithm, Research Report. 124, Digital Systems Research Center, Palo Alto, California, May 1994
6. M. Farach, Optimal Suffix Tree Construction with Large Alphabets, in: 38th IEEE Symp. on Foundations of Computer Science, 1997, pp. 137-143
7. P. Ferragina, G. Manzini, Optimal compression boosting in optimal linear time using the Burrows-Wheeler transform, in: Proceedings of the Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2004
8. Ferragina P., and Manzini G. Indexing compressed texts. Journal of the ACM 52 4 (2005) 552-581
9. Gonnet G.H., and Baeza-Yates R.A. Handbook of Algorithms and Data Structures (1991), Addison-Wesley
10. 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
11. Hoare C.A.R. Quicksort. Computer Journal 5 (1962) 10-15
12. Hon W.K., Lam T.W., Sadakane K., and Sung W.K. Constructing compressed suffix arrays with large alphabets. Proc. of ISAAC. LNCS vol. 2906 (2003) 240-249
13. Hon W.K., Sadakane K., and Sung W.K. Breaking a time-and-space barrier in constructing full-text indices. Proc. IEEE FOCS (2003) 251-260
14. H. Itoh, H. Tanaka, An Efficient Method for in Memory Construction of Suffix Arrays, in: Proc. IEEE String Processing and Information Retrieval Symposium (SPIRE'99), 1999, pp. 81-88
15. Kärkkäinen J., Sanders P., and Burkhardt S. Simple linear work suffix array construction. Journal of the ACM 53 6 (2006) 918-936
16. Richard M. Karp, Raymond E. Miller, Arnold L. Rosenberg, Rapid identification of repeated patterns in strings, trees and arrays, in: Proceedings of the 5th Annual IEEE Symposium on Foundations of Computer Science, 1972, pp. 125-136
17. Kernighan B.W., and Ritchie D.M. The C Programming Language. second ed. (1988), Prentice Hall
18. Kim D., Sim J., Park H., and Park K. Linear-Time construction of suffix arrays. Proc. CPM. LNCS vol. 2676 (2003) 186-199
19. Ko P., and Aluru S. Space efficient linear time construction of suffix arrays. Proc. CPM. LNCS vol. 2676 (2003) 200-210
20. Manber U., and Myers G. Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22 5 (1993) 935-948
21. M. Maniscalco, MSufSort, 2005, http://www.michael-maniscalco.com/ msufsort.htm
22. Manzini G. An analysis of the Burrows-Wheeler transform. Journal of the ACM 48 3 (2001) 407-430
23. Manzini G., and Ferragina P. Engineering a lightweight suffix array construction algorithm. Algorithmica 40 1 (2004) 33-50
24. Peter M. McIlroy, M. Douglas McIlroy, ssarray.c, Source Code, 1997, http://www.cs.dartmouth.edu/~doug/sarray/
25. S. Puglisi, W. Smyth, A. Turpin, A taxonomy of suffix array construction algorithms, in: Proc. Prague Stringology Conference, 2005
26. S. Puglisi, W. Smyth, A. Turpin, The performance of linear time suffix sorting algorithms (extended abstract), in: Proc. DCC, IEEE, 2005, pp. 358-367
27. Kunihiko Sadakane, A fast algorithm for making suffix arrays and for Burrows-Wheeler transformation, in: Proceedings of the IEEE Data Compression Conference, 1998, pp. 129-138
28. M. Schindler, szip homepage, 1998, http://www.compressconsult.com/szip/
29. Schönhage A., Paterson M., and Pippenger N. Finding the median. Journal of Computer and System Sciences 13 2 (1976) 184-199
30. J. Seward, bzip2, 1996, http://www.bzip.org/
31. Peter Weiner, Linear pattern matching algorithms, in: Proceedings of the 14th Annual IEEE Symposium on Foundations of Computer Science, 1973, pp. 1-11