Engineering a compressed suffix tree implementation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4525 LNCS, Issue , 2007, Pages 217-228

  Välimäki, Niko ^a   Gerlach, Wolfgang ^b   Dixit, Kashyap ^c   Mäkinen, Veli ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b BIELEFELD UNIVERSITY   (Germany)

^c INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CHARACTER RECOGNITION; COMPUTATIONAL METHODS; DATA COMPRESSION;

ALPHABETS; BIOLOGICAL SEQUENCES; MEMORY SIZE;

TREES (MATHEMATICS);

EID: 37249088071     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-72845-0_17     Document Type: Conference Paper

References (26)

1. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms 2, 53-86 (2004)
2. Apostolico, A.: The myriad virtues of subword trees. In: Combinatorial Algorithms on Words, NATO ISI Series pp. 85-96. Springer, Heidelberg (1985)
3. Burrows, M., Wheeler, D.: A block sorting lossless data compression algorithm. Technical Report Technical Report 124, Digital Equipment Corporation (1994)
4. Chan, W.-L., Hon, W.-K., Lam, T.-W.: Compressed index for a dynamic collection of texts. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 445-456. Springer, Heidelberg (2004)
5. Cheung, C.-F., Yu, J.X., Lu, H.: Constructing suffix tree for gigabyte sequences with megabyte memory. IEEE Transactions on Knowledge and Data Engineering 17(1), 90-105 (2005)
6. Crochemore, M., Rytter, W.: Jewels of Stringology. World Scientific, Singapore (2002)
7. Elias, P.: Universal codeword sets and representation of the integers. IEEE Transactions on Information Theory 21(2), 194-200 (1975)
8. Farach-Colton, M., Bender, M.A.: The lca problem revisited. In: Gonnet, G.H., Viola, A. (eds.) LATIN 2000. LNCS, vol. 1776, pp. 88-94. Springer, Heidelberg (2000)
9. Ferragina, P., Manzini, C.: Indexing compressed texts. Journal of the ACM 52(4), 552-581 (2005)
10. González, R., Grabowski, Sz., Mäkinen, V., Navarro, G.: Practical implementation of rank and select queries. In: Nikoletseas, S.E. (ed.) WEA 2005. LNCS, vol. 3503, pp. 27-38. Springer, Heidelberg (2005)
11. Grossi, R., Gupta, A., Vitter, J.: High-order entropy-compressed text indexes. In: Proc. SODA'03, pp. 841-850 (2003)
12. Grossi, R., Vitter, J.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM Journal on Computing 35(2), 378-407 (2006)
13. Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)
14. Hon, W.-K.: On the Construction and Application of Compressed Text Indexes. PhD thesis, University of Hong Kong (2004)
15. Hon, W.-K., Sadakane, K.: Space-economical algorithms for finding maximal unique matches. In: Apostolico, A., Takeda, M. (eds.) CPM 2002. LNCS, vol. 2373, pp. 144-152. Springer, Heidelberg (2002)
16. Hon, W.-K., Sadakane, K., Sung, W.-K.: Breaking a time-and-space barrier in constructing full-text indices. In: Proc. FOCS'03, p. 251 (2003)
17. Kasai, T., Lee, G., Arimura, H., Arikawa, S., Park, K.: Linear-time longest-common-prefix computation in suffix arrays and its applications. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 181-192. Springer, Heidelberg (2001)
18. Mäkinen, V., Navarro, G.: Succinct suffix arrays based on run-length encoding. Nordic Journal of Computing 12(1), 40-66 (2005)
19. Mäkinen, V., Navarro, G.: Dynamic entropy compressed sequences and full-text indexes. In: Lewenstein, M., Valiente, G. (eds.) CPM 2006. LNCS, vol. 4009, pp. 306-317. Springer, Heidelberg (2006)
20. Manber, U., Myers, G.: Suffix arrays: a new method for on-line string searches. SIAM Journal on Computing, pp. 935-948 (1993)
21. Munro, I.: Tables. In: Chandru, V., Vinay, V. (eds.) Foundations of Software Technology and Theoretical Computer Science (FSTTCS'96). LNCS, vol. 1180, pp. 37-42. Springer, Heidelberg (1996)
22. Munro, I., Raman, V., Rao, S.: Space efficient suffix trees. Journal of Algorithms 39(2), 205-222 (2001)
23. Navarro, G.: Indexing text using the Ziv-Lempel trie. Journal of Discrete Algorithms (JDA) 2(1), 87-114 (2004)
24. Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Computing Surveys, 2007. To appear, preliminary version available at ftp://ftp.dcc.uchile.cl/pub/users/gnavarro/survcompr2.ps.gz
25. Sadakane, K.: Compressed suffix trees with full functionality. Theory of Computing Systems, 2007. To appear, preliminary version available at http://tcslab.csce.kyushu-u.ac.jp/-sada/papers/cst.ps
26. Schürmann, K.-B., Stoye, J.: An incomplex algorithm for fast suffix array construction. In: Proc. ALENEX/ANALCO, pp. 77-85 (2005)