Matching statistics: Efficient computation and a new practical algorithm for the multiple common substring problem

Software - Practice and Experience

Volumn 36, Issue 3, 2006, Pages 305-331

  Maaß, Moritz G ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Algorithms and data structures; Common substring problem; Matching statistics; Pattern matching; Suffix array; Suffix tree

Indexed keywords

ARRAYS; COMPUTATION THEORY; PROBLEM SOLVING; STATISTICS;

ALGORITHMS AND DATA STRUCTURES; COMMON SUBSTRING PROBLEM; MATCHING STATISTICS; SUFFIX ARRAY; SUFFIX TREE;

ALGORITHMS;

EID: 33644794894     PISSN: 00380644     EISSN: 1097024X     Source Type: Journal    
DOI: 10.1002/spe.698     Document Type: Article

References (32)

1. Gusfield D. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. Press Syndicate of the University of Cambridge, 1997.
2. Maaß MG. A fast algorithm for the inexact characteristic string problem. Technical Report TUM-10312, Fakultät für Informatik, TU München, August 2003.
3. Hui L. Color set size problem with applications to string matching. Proceedings of the 3rd Symposium on Combinatorial Pattern Matching (CPM) (Lecture Notes in Computer Science, vol. 644). Springer: Berlin, 1992; 230-243.
4. Schieber B, Vishkin U. On finding lowest common ancestors: Simplification and parallelization. SIAM Journal of Computing 1988; 17(6): 1253-1262.
5. Höhl M, Kurtz S, Ohlebusch E. Efficient multiple genome alignment. Bioinformatics 2002; 18(1):312-320.
6. Kasai T, Lee G, Arimura H, Arikawa S, Park K. Linear-time longest-common-prefix computation in suffix arrays and its applications. Proceedings of the 12th Symposium on Combinatorial Pattern Matching (CPM) (Lecture Notes in Computer Science, vol. 2089), Amir A, Landau GM (eds.). Springer: Berlin, 2001; 181-192.
7. Chang WI, Lawler EL. Sublinear approximate string matching and biological applications. Algorithmica 1994; 12:327-344.
8. Ukkonen E. On-line construction of suffix trees. Algorithmica 1995; 14:249-260.
9. Manber U, Myers G. Suffix arrays: A new method for on-line string searches. SIAM Journal of Computing 1993; 22(5):935-948.
10. Grossi R, Vitter JS. Compressed suffix arrays and suffix trees with applications to text indexing and string matching. Proceedings of the 32nd Symposium on Theory of Computing (STOC). ACM Press: New York, 2000; 397-406.
11. Sadakane K. Compressed text databases with efficient query algorithms based on the compressed suffix array. Proceedings of the 11th International Symposium on Algorithms and Computation (ISAAC) (Lecture Notes in Computer Science, vol. 1969), Lee DT, Teng S-H (eds.). Springer: Berlin, 2000; 410-421.
12. Abouelhoda MI, Kurtz S, Ohlebusch E. The enhanced suffix array and its applications to genome analysis. Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI) (Lecture Notes in Computer Science, vol. 2452). Springer: Berlin, 2002; 449-463.
13. Abouelhoda MI, Ohlebusch E, Kurtz S. Optimal exact string matching based on suffix arrays. Proceedings of the 9th International Symposim on String Processing and Information Retrieval (SPIRE) (Lecture Notes in Computer Science, vol. 2476), Laender AHF, Oliveira AL (eds.). Springer: Berlin, 2002; 31-43.
14. Kim DK, Jeon JE, Park H. An efficient index data structure with the capabilities of suffix trees and suffix arrays for alphabets of non-negligible size. Proceedings of the 11th International Conference on String Processing and Information Retrieval (SPIRE) (Lecture Notes in Computer Science, vol. 3246). Springer: Berlin, 2004; 138-149.
15. Kärkkäinen J, Sanders P. Simple linear work suffix array construction. Proceedings of the 30th International Colloqium on Automata, Languages and Programming (ICALP) (Lecture Notes in Computer Science, vol. 2719). Springer: Berlin, 2003; 943-955.
16. Kim DK, Sim JS, Park H, Park K. Linear-time construction of suffix arrays. Proceedings of the 14th Symposium on Combinatorial Pattern Matching (CPM) (Lecture Notes in Computer Science, vol. 2676), Baeza-Yates RA, Chávez E, Crochemore M (eds.). Springer: Berlin, 2003; 186-199.
17. Ko P, Aluru S. Space efficient linear time construction of suffix arrays. Proceedings of the 14th Symposium on Combinatorial Pattern Matching (CPM) (Lecture Notes in Computer Science, vol. 2676), Baeza-Yates RA, Chávez E, Crochemore M (eds.). Springer: Berlin, 2003; 200-210.
18. Kim DK, Jo J, Park H. A fast algorithm for constructing suffix arrays for fixed-size alphabets. Proceedings of the 3rd International Workshop on Experimental and Efficient Algorithms (WEA) (Lecture Notes in Computer Science, vol. 3059). Springer: Berlin, 2004; 301-314.
19. Jesper Larsson N, Sadakane K. Faster suffix sorting. Technical Report LU-CS-TR.-99-214, Department of Computer Science, Lund University, Sweden, 1999.
20. Manzini G, Ferragina P. Engineering a lightweight suffix array construction algorithm. Proceedings of the 10th European Symposium on Algorithms (ESA), Rome, Italy, 2002 (Lecture Notes in Computer Science, vol. 2461). Springer: Berlin, 2002; 698-710.
21. Burkhardt S, Kärkkäinen J. Fast lightweight suffix array construction and checking. Proceedings of the 14th Symposium on Combinatorial Pattern Matching (CPM) (Lecture Notes in Computer Science, vol. 2676). Springer: Berlin, 2003; 55-69.
22. Giegerich R, Kurtz S. From Ukkonen to McCreight and Weiner: A unifying view of linear-time suffix tree construction. Algorithmica 1997; 19:331-353.
23. McCreight EM. A space-economical suffix tree construction algorithm. Journal of the ACM 1976; 23(2):262-272.
24. Kurtz S. Reducing the space requirement of suffix trees. Software - Practice and Experience 1999; 29(13):1149-1171.
25. Giegerich R, Kurtz S, Stoye J. Efficient implementation of lazy suffix trees. Software - Practice and Experience 2003; 33:1035-1049.
26. Abouelhoda MI, Kurtz S, Ohlebusch E. Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms 2004; 2:53-86.
27. Manzini G, Ferragina P. Engineering a lightweight suffix array construction algorithm. Algorithmica 2004; 40(1):33-50.
28. Wyner AD, Ziv J. Some asymptotic properties of the entropy of stationary ergodic data source with applications to data compression. IEEE Transactions on Information Theory 1989; 35(6):1250-1258.
29. Szpankowski W. A generalized suffix tree and its (un)expected asymptotic behaviors. SIAM Journal of Computing 1993; 22:1176-1198.
30. Szpankowski W. Asymptotic properties of data compression and suffix trees. IEEE Transactions on Information Theory 1993; 39(5):1647-1659.
31. Szpankowski W. Average Case Analysis of Algorithms on Sequences. Wiley-Interscience: New York, 2000.
32. Blumer A, Ehrenfeucht A, Haussler D. Average sizes of suffix trees and DAWGs. Discrete Applied Mathematics 1989; 24(1):37-45.