Fast BWT in small space by blockwise suffix sorting

Theoretical Computer Science

Volumn 387, Issue 3, 2007, Pages 249-257

  Kärkkäinen, Juha ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Burrows Wheeler transform; Space efficient algorithms; Suffix array; Suffix sorting

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; MATHEMATICAL TRANSFORMATIONS;

BURROWS-WHEELER TRANSFORM; SPACE-EFFICIENT ALGORITHMS; SUFFIX ARRAY; SUFFIX SORTING;

SORTING;

EID: 35449006300     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2007.07.018     Document Type: Article

References (28)

1. Bentley J.L., and Sedgewick R. Fast algorithms for sorting and searching strings. Proc. 8th Annual Symposium on Discrete Algorithms (1997), ACM
2. Burkhardt S., and Kärkkäinen J. Fast lightweight suffix array construction and checking. Proc. 14th Annual Symposium on Combinatorial Pattern Matching. LNCS vol. 2676 (2003), Springer
3. M. Burrows, D.J. Wheeler, A block-sorting lossless data compression algorithm, Technical Report 124, SRC (digital, Palo Alto), May 1994
4. Crauser A., and Ferragina P. Theoretical and experimental study on the construction of suffix arrays in external memory. Algorithmica 32 1 (2002) 1-35
5. R. Dementiev, J. Kärkkäinen, J. Mehnert, P. Sanders, Better external memory suffix array construction, ACM Journal of Experimental Algorithmics (in press)
6. Ferragina P., and Manzini G. Indexing compressed text. Journal of the ACM 52 4 (2005) 552-581
7. Ferragina P., Manzini G., Mäkinen V., and Navarro G. Compressed representations of sequences and full-text indexes. ACM Transactions on Algorithms 3 2 (2007) Article 20, 24 pages
8. Fredriksson K. Faster string matching with super-alphabets. Proc. 9th Symposium on String Processing and Information Retrieval. LNCS vol. 2476 (2002), Springer
9. Grossi R., and Italiano G.F. Efficient techniques for maintaining multidimensional keys in linked data structures (extended abstract). Proc. 26th International Conference on Automata, Languages and Programming. LNCS vol. 1644 (1999), Springer
10. Hon W.-K., Lam T.-W., Sadakane K., and Sung W.-K. Constructing compressed suffix arrays with large alphabets. Proc. 14th International Symposium on Algorithms and Computation. LNCS vol. 2906 (2003), Springer
11. W.-K. Hon, T.-W. Lam, W.-K. Sung, W.-L. Tse, C.-K. Wong, S.-M. Yiu, Practical aspects of compressed suffix arrays and FM-index in searching DNA sequences, in: Proc. 6th Workshop on Algorithm Engineering and Experiments, ALENEX '04, 2004
12. Hon W.-K., Sadakane K., and Sung W.-K. Breaking a time-and-space barrier in constructing full-text indices. Proc. 44th Annual Symposium on Foundations of Computer Science (2003), IEEE
13. Itoh H., and Tanaka H. An efficient method for in memory construction of suffix arrays. Proc. 6th Symposium on String Processing and Information Retrieval (1999), IEEE
14. Jacquet P., and Szpankowski W. Autocorrelation on words and its applications - Analysis of suffix trees by string-ruler approach. Journal of Combinatorial Theory, Series A 66 2 (1994) 237-269
15. Kärkkäinen J., and Rao S.S. Full-text indexes in external memory. In: Meyer U., Sanders P., and Sibeyn J. (Eds). Algorithms for Memory Hierarchies (Advanced Lectures). LNCS vol. 2625 (2003), Springer 149-170 (Chapter 7)
16. Kärkkäinen J., and Sanders P. Simple linear work suffix array construction. Proc. 30th International Conference on Automata, Languages and Programming. LNCS vol. 2719 (2003), Springer
17. Kärkkäinen J., Sanders P., and Burkhardt S. Linear work suffix array construction. Journal of the ACM 53 6 (2006) 918-936
18. 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
19. Ko P., and Aluru S. Space efficient linear time construction of suffix arrays. Journal of Discrete Algorithms 3 2-4 (2005) 143-156
20. Lam T.-W., Sadakane K., Sung W.-K., and Yiu S.-M. A space and time efficient algorithm for constructing compressed suffix arrays. Proc. 8th Annual International Conference on Computing and Combinatorics. LNCS vol. 2387 (2002), Springer
21. Navarro G., and Mäkinen V. Compressed full-text indexes. ACM Computing Surveys 39 1 (2007) Article 2, 61 pages
22. Manber U., and Myers G. Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22 5 (1993) 935-948
23. M.A. Maniscalco, S.J. Puglisi, Faster lightweight suffix array construction, in: Proc. 17th Australasian Workshop on Combinatorial Algorithms, 2006
24. Manzini G. An analysis of the Burrows-Wheeler transform. Journal of the ACM 48 3 (2001) 407-430
25. Manzini G., and Ferragina P. Engineering a lightweight suffix array construction algorithm. Algorithmica 40 1 (2004) 33-50
26. Na J.C. Linear-time construction of compressed suffix arrays using o (n log n)-bit working space for large alphabets. Proc. 16th Annual Symposium on Combinatorial Pattern Matching. LNCS vol. 3537 (2005), Springer
27. Puglisi S.J., Smyth W.F., and Turpin A.H. A taxonomy of suffix array construction algorithms. ACM Computing Surveys 39 2 (2007) Article 4, 31 pages
28. Seward J. On the performance of BWT sorting algorithms. Proc. Data Compression Conference (2000), IEEE