Approximate string matching with compressed indexes

Algorithms

Volumn 2, Issue 3, 2009, Pages 1105-1136

  Russo, Luís M S ^a,c   Navarro, Gonzalo ^b   Oliveira, Arlindo L ^a,d   Morales, Pedro ^b  

^a INESC ID   (Portugal)

^b UNIVERSITY OF CHILE   (Chile)

^c UNIVERSIDADE NOVA DE LISBOA   (Portugal)

^d INSTITUTO SUPERIOR TÉCNICO   (Portugal)

Author keywords

Approximate string matching; Compressed index; Compressed suffix array; Compressed suffix tree; Lempel ziv

Indexed keywords

EID: 78449269708     PISSN: None     EISSN: 19994893     Source Type: Journal    
DOI: 10.3390/a2031105     Document Type: Article

References (58)

1. Navarro, G. A guided tour to approximate string matching. ACM Comput. Surv. 2001, 33, 31-88.
2. Chang, W.; Marr, T. Approximate string matching and local similarity. In Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching (CPM), Asilomar, CA, USA, June 5-8, 1994; pp. 259-273.
3. Fredriksson, K.; Navarro, G. Average-optimal single and multiple approximate string matching. ACM J. Exp. Algorithmics 2004, 9, No. 1.4.
4. Navarro, G.; Baeza-Yates, R.; Sutinen, E.; Tarhio, J. Indexing methods for approximate string matching. IEEE Data Eng. Bull. 2001, 24, 19-27.
5. Sung, W.K. Indexed approximate string matching; Springer: Berlin, Germany, 2008; pp. 408-411.
6. Cole, R.; Gottlieb, L.A.; Lewenstein, M. Dictionary matching and indexing with errors and don't cares. In Proceedings of the 36th ACM Symposium on Theory of Computing (STOC), Chicago, IL, USA, June 13-16, 2004; pp. 91-100.
7. Maaß, M.; Nowak, J. Text indexing with errors. In Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM), Jeju Island, Korea, June 19-22, 2005; pp. 21-32.
8. Chan, H.L.; Lam, T.W.; Sung, W.K.; Tam, S.L.;Wong, S.S. A linear size index for approximate pattern matching. In Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM), Barcelona, Spain, July 5-7, 2006; pp. 49-59.
9. Coelho, L.; Oliveira, A. Dotted suffix trees: a structure for approximate text indexing. In Proceed ings of the 13th International Symposium on String Processing and Information Retrieval (SPIRE), Glasgow, UK, October 11-13, 2006; pp. 329-336.
10. Weiner, P. Linear pattern matching algorithms. In 14th IEEE Annual Symposium on Switching and Automata Theory, Iowa City, USA, October 15-17, 1973; pp. 1-11.
11. Manber, U.; Myers, E. Suffix arrays: a new method for on-line string searches. SIAM J. Comput. 1993, 22, 935-948.
12. Gonnet, G. A tutorial introduction to Computational Biochemistry using Darwin; Technical report; Informatik E.T.H.: Zuerich, Switzerland, 1992.
13. Ukkonen, E. Approximate string matching over suffix trees. In Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching (CPM), Asilomar, CA, USA, June 5-8, 1994; pp. 228-242.
14. Cobbs, A. Fast approximate matching using suffix trees. In Proceedings of the 6th Annual Symposium on Combinatorial Pattern Matching (CPM), Espoo, Finland, July 5-7, 1995; pp. 41-54.
15. Sutinen, E.; Tarhio, J. Filtration with q-samples in approximate string matching. In Proceeding of the 7th Annual Symposium on Combinatorial Pattern Matching (CPM), Laguna Beach, CA, USA, June 10-12, 1996; pp. 50-63.
16. Navarro, G.; Baeza-Yates, R. A practical q-gram index for text retrieval allowing errors. CLEI Electron. J. 1998, 1, No. 2.
17. Myers, E.W. A sublinear algorithm for approximate keyword searching. Algorithmica 1994, 12, 345-374.
18. Navarro, G.; Baeza-Yates, R. A hybrid indexing method for approximate string matching. J. Discrete Algorithms 2000, 1, 205-239.
19. Navarro, G.; Sutinen, E.; Tarhio, J. Indexing text with approximate q-grams. J. Discrete Algorithms 2005, 3, 157-175.
20. Kurtz, S. Reducing the space requirement of suffix trees. Softw. Pract. Exper. 1999, 29, 1149-1171.
21. Navarro, G.; Mäkinen, V. Compressed full-text indexes. ACM Comput. Surv. 2007, 39, No. 2.
22. Manzini, G. An analysis of the Burrows-Wheeler transform. JACM 2001, 48, 407-430.
23. Ziv, J.; Lempel, A. Compression of individual sequences via variable length coding. IEEE Trans. Inf. Theory 1978, 24, 530-536.
24. Ferragina, P.; Manzini, G. Indexing compressed text. JACM 2005, 52, 552-581.
25. Navarro, G. Indexing text using the Ziv-Lempel trie. J. Discrete Algorithms 2004, 2, 87-114.
26. Kärkkäinen, J.; Ukkonen, E. Lempel-Ziv parsing and sublinear-size index structures for string matching. In Proceedings of the 3rd South AmericanWorkshop on String Processing (WSP), Recife, Brazil, August 08-09, 1996; pp. 141-155.
27. Arroyuelo, D.; Navarro, G.; Sadakane, K. Reducing the space requirement of LZ-Index. In Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM), Barcelona, Spain, July 5-7, 2006; pp. 318-329.
28. Russo, L.M.S.; Oliveira, A.L. A compressed self-index using a Ziv-Lempel dictionary. Inf. Retr. 2008, 11, 359-388.
29. Sadakane, K. New text indexing functionalities of the compressed suffix arrays. J. Algorithms 2003, 48, 294-313.
30. Grossi, R.; Gupta, A.; Vitter, J. High-order entropy-compressed text indexes. In Proceedings of the 14th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Baltimore, MD, USA, January 12-14 2003; pp. 841-850.
31. Ferragina, P.; Manzini, G.; Mäkinen, V.; Navarro, G. Compressed representations of sequences and full-text indexes. ACM Trans. Algorithms 2007, 3, No. 20.
32. Grossi, R.; Vitter, J. Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comput. 2005, 35, 378-407.
33. Sadakane, K. Compressed suffix trees with full functionality. Theory Comput. Syst. 2007, 41, 589-607.
34. Fischer, J.; Mäkinen, V.; Navarro, G. An(other) entropy-bounded compressed suffix tree. In Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), Pisa, Italy, June 18-20, 2008; pp. 152-165.
35. Russo, L.; Navarro, G.; Oliveira, A. Fully-compressed suffix trees. In Proceedings of the 8th Latin American Symposium on Theoretical Informatics (LATIN), Búzios, Brazil, April 7-11, 2008; pp. 362-373.
36. Ferragina, P.; González, R.; Navarro, G.; Venturini, R. Compressed text indexes: From theory to practice. ACM J. Exp. Algorithmics (JEA) 2009, 13, No. 12.
37. Huynh, T.; Hon, W.K.; Lam, T.W.; Sung, W.K. Approximate string matching using compressed suffix arrays. In Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM), Jeju Island, Korea, June 19-22, 2005; pp. 434-444.
38. Lam, T.W.; Sung, W.K.; Wong, S.S. Improved approximate string matching using compressed suffix data structures. In Proceedings of the 16th Annual International Symposium on Algorithms and Computation (ISAAC), Hainan, China, December 19-21, 2005; pp. 339-348.
39. Navarro, G.; Baeza-Yates, R. Improving an algorithm for approximate pattern matching. Algorithmica 2001, 30, 473-502.
40. Russo, L.M.S.; Navarro, G.; Oliveira, A.L. Approximate string matching with Lempel-Ziv compressed indexes. In Proceedings of the 14th International Symposium on String Processing and Information Retrieval (SPIRE), Santiago, Chile, October 29-31, 2007; pp. 264-275.
41. Russo, L.M.S.; Navarro, G.; Oliveira, A.L. Indexed hierarchical approximate string matching. In Proceedings of the 15th International Symposium on String Processing and Information Retrieval (SPIRE), Melbourne, Australia, November 10-12, 2008; pp. 144-154.
42. Apostolico, A. The myriad virtues of subword trees. In Combinatorial Algorithms on Words; Springer-Verlag: New York, NY, USA, 1985; pp. 85-96.
43. Gusfield, D. Algorithms on Strings, Trees and Sequences; Cambridge University Press, Cambridge, UK, 1997.
44. Lempel, A.; Ziv, J. On the complexity of finite sequences. IEEE Trans. Inf. Theory 1976, 22, 75-81.
45. Ziv, J.; Lempel, A. A universal algorithm for sequential data compression. IEEE Trans. Inf. Theory 1977, 23, 337-343.
46. Welch, T. A technique for high performance data compression. IEEE Comput. Mag. 1984, 17, 8-19.
47. Ukkonen, E. Finding approximate patterns in strings. J. Algorithms 1985, 6, 132-137.
48. Landau, G.M.; Myers, E.W.; Schmidt, J.P. Incremental string comparison. SIAM J. Comput. 1998, 27, 557-582.
49. Maaß, M. Linear bidirectional on-line construction of affix trees. Algorithmica 2003, 37, 43-74.
50. Navarro, G. Implementing the lz-index: Theory versus practice. ACM J. Exp. Algorithmics 2009, 13, No. 2.
51. Ukkonen, E. Finding approximate patterns in strings. J. Algorithms 1985, 6, 132-137.
52. Navarro, G.; Baeza-Yates, R. A hybrid indexing method for approximate string matching. J. Discrete Algorithms 2000, 1, 205-239.
53. Lee, S.; Park, K. Dynamic rank-select structures with applications to run-length encoded texts. In Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), Pisa, Italy, June 18-20, 2008; pp. 95-106.
54. Myers, G. A fast bit-vector algorithm for approximate string matching based on dynamic programming. JACM 1999, 46, 395-415.
55. Navarro, G.; Baeza-Yates, R. Very fast and simple approximate string matching. Inf. Proc. Lett. 1999, 72, 65-70.
56. Raman, R.; Raman, V.; Rao, S.S. Succinct indexable dictionaries with applications to encoding k-ary trees and multisets. In Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms, San Francisco, CA, USA, January 6-8, 2002; pp. 233-242.
57. Mäkinen, V.; Navarro, G. Dynamic entropy-compressed sequences and full-text indexes. ACM Trans. Algorithms 2008, 4, 32:1-32:38.
58. Wu, S.; Manber, U. Fast text searching allowing errors. Commun. ACM 1992, 35, 83-91.