Approximate string matching with Lempel-Ziv compressed indexes

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

Volumn 4726 LNCS, Issue , 2007, Pages 264-275

  Russo, Luís M S ^a   Navarro, Gonzalo ^b   Oliveira, Arlindo L ^a  

^a INESC ID   (Portugal)

^b UNIVERSITY OF CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA COMPRESSION; DATA STRUCTURES; INDEXING (OF INFORMATION); PROBLEM SOLVING;

APPROXIMATE STRING MATCHING (ASM); FULL-TEXT SELF-INDEX; LEMPEL-ZIV INDEX;

PATTERN MATCHING;

EID: 38049048329     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-75530-2_24     Document Type: Conference Paper

References (34)

1. Navarro, G.: A guided tour to approximate string matching. ACM Comput. Surv. 33(1), 31-88 (2001)
2. Chang, W.I., Marr, T.C.: Approximate string matching and local similarity. In: Crochemore, M., Gusfield, D. (eds.) CPM 1994. LNCS, vol. 807, pp. 259-273. Springer, Heidelberg (1994)
3. Fredriksson, K., Navarro, G.: Average-optimal single and multiple approximate string matching. ACM Journal of Experimental Algorithmics 9(1.4) (2004)
4. Navarro, G., Baeza-Yates, R., Sutinen, E., Tarhio, J.: Indexing methods for approximate string matching. IEEE Data Engineering Bulletin 24(4), 19-27 (2001)
5. Cole, R., Gottlieb, L.A., Lewenstein, M.: Dictionary matching and indexing with errors and don't cares. In: STOC, pp. 91-100 (2004)
6. Maaß, M., Nowak, J.: Text indexing with errors. In: CPM, pp. 21-32 (2005)
7. Chan, H.L., Lam, T.W., Sung, W.K., Tam, S.L., Wong, S.S.: A linear size index for approximate pattern matching. In: Lewenstein, M., Valiente, G. (eds.) CPM 2006. LNCS, vol. 4009, pp. 49-59. Springer, Heidelberg (2006)
8. Coelho, L., Oliveira, A.: Dotted suffix trees: a structure for approximate text indexing. In: Crestani, F., Ferragina, P., Sanderson, M. (eds.) SPIRE 2006. LNCS, vol. 4209, pp. 329-336. Springer, Heidelberg (2006)
9. Weiner, P.: Linear pattern matching algorithms. In: IEEE 14th Annual Symposium on Switching and Automata Theory, pp. 1-11. IEEE Computer Society Press, Los Alamitos (1973)
10. Manber, U., Myers, E.: Suffix arrays: a new method for on-line string searches. SIAM Journal on Computing, 935-948 (1993)
11. Gonnet, G.: A tutorial introduction to Computational Biochemistry using Darwin. Technical report, Informatik E.T.H., Zuerich, Switzerland (1992)
12. Ukkonen, E.: Approximate string matching over suffix trees. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds.) Combinatorial Pattern Matching. LNCS, vol. 684, pp. 228-242. Springer, Heidelberg (1993)
13. Cobbs, A.: Fast approximate matching using suffix trees. In: Galil, Z., Ukkonen, E. (eds.) Combinatorial Pattern Matching. LNCS, vol. 937, pp. 41-54. Springer, Heidelberg (1995)
14. Sutinen, E., Tarhio, J.: Filtration with q-samples in approximate string matching. In: Hirschberg, D.S., Meyers, C (eds.) CPM 1996. LNCS, vol. 1075, pp. 50-63. Springer, Heidelberg (1996)
15. Navarro, G., Baeza-Yates, R.: A practical q-gram index for text retrieval allowing errors. CLEI Electronic Journal 1(2) (1998)
16. Myers, E.W.: A sublinear algorithm for approximate keyword searching. Algorithmica 12(4/5), 345-374 (1994)
17. Navarro, G., Baeza-Yates, R.: A hybrid indexing method for approximate string matching. Journal of Discrete Algorithms 1(1), 205-239 (2000)
18. Navarro, C., Sutinen, E., Tarhio, J.: Indexing text with approximate q-grams. J. Discrete Algorithms 3(2-4), 157-175 (2005)
19. Kurtz, S.: Reducing the space requirement of suffix trees. Pract. Exper. 29(13), 1149-1171 (1999)
20. Sadakane, K.: New text indexing functionalities of the compressed suffix arrays. J. Algorithms 48(2), 294-313 (2003)
21. Ferragina, P., Manzini, G.: Indexing compressed text. Journal of the ACM 52(4), 552-581 (2005)
22. Navarro, G.: Indexing text using the Ziv-Lempel trie. J. Discrete Algorithms 2(1), 87-114 (2004)
23. Grossi, R., Vitter, J.S.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comput. 35(2), 378-407 (2005)
24. Navarro, C., Mäkinen, V.: Compressed full-text indexes. ACM Computing Surveys 39(1) article 2 (2007)
25. Manzini, G.: An analysis of the Burrows-Wheeler transform. Journal of the ACM 48(3), 407-430 (2001)
26. Kärkkäinen, J., Ukkonen, E.: Lempel-Ziv parsing and sublinear-size index structures for string matching. In: South American Workshop on String Processing, pp. 141-155. Carleton University Press (1996)
27. Arroyuelo, D., Navarro, C., Sadakane, K.: Reducing the space requirement of LZ-Index. In: Lewenstein, M., Valiente, C. (eds.) CPM 2006. LNCS, vol. 4009, pp. 318-329. Springer, Heidelberg (2006)
28. Russo, L.M.S., Oliveira, A.L.: A compressed self-index using a Ziv-Lempel dictionary. In: Crestani, F., Ferragina, P., Sanderson, M. (eds.) SPIRE 2006. LNCS, vol. 4209, pp. 163-180. Springer, Heidelberg (2006)
29. Huynh, T., Hon, W., Lam, T., Sung, W.: Approximate string matching using compressed suffix arrays. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 434-444. Springer, Heidelberg (2004)
30. Lam, T., Sung, W., Wong, S.: Improved approximate string matching using compressed suffix data structures. In: Deng, X., Du, D.-Z. (eds.) ISAAC 2005. LNCS, vol. 3827, pp. 339-348. Springer, Heidelberg (2005)
31. Morales, P.: Solución de consultas complejas sobre un indice de texto comprimido (solving complex queries over a compressed text index). Undergraduate thesis, Dept. of Computer Science, University of Chile, G. Navarro, advisor (2005)
32. Ziv, J., Lempel, A.: Compression of individual sequences via variable length coding. IEEE Transactions on Information Theory 24(5), 530-536 (1978)
33. Myers, G.: A fast bit-vector algorithm for approximate string matching based on dynamic programming. Journal of the ACM 46(3), 395-415 (1999)
34. Navarro, G., Baeza-Yates, R.: Very fast and simple approximate string matching. Information Processing Letters 72, 65-70 (1999)