Pattern matching with address errors: Rearrangement distances

Journal of Computer and System Sciences

Volumn 75, Issue 6, 2009, Pages 359-370

  Amir, Amihood ^a,b   Aumann, Yonatan ^a   Benson, Gary ^c   Levy, Avivit ^a   Lipsky, Ohad ^a   Porat, Ely ^a   Skiena, Steven ^d   Vishne, Uzi ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b Johns Hopkins University   (United States)

^c BOSTON UNIVERSITY   (United States)

^d Stony Brook University   (United States)

Author keywords

Address metrics; Approximate pattern matching; Rearrangement errors; Swaps

Indexed keywords

ERRORS; PATTERN MATCHING;

ADDRESS METRICS; APPROXIMATE PATTERN MATCHING; PATTERN MATCHING PROBLEMS; STRING MATCHING; SWAPS;

STRING SEARCHING ALGORITHMS;

EID: 67349275041     PISSN: 00220000     EISSN: 10902724     Source Type: Journal    
DOI: 10.1016/j.jcss.2009.03.001     Document Type: Article

References (31)

1. Abrahamson K. Generalized string matching. SIAM J. Comput. 16 6 (1987) 1039-1051
2. A. Amir, A. Aumann, R. Cole, M. Lewenstein, E. Porat, Function matching: Algorithms, applications, and a lower bound, in: Proc. 30th ICALP, 2003, pp. 929-942
3. A. Amir, Y. Aumann, A. Levy, Approximate string matching with address bit errors, manuscript
4. Amir A., Cole R., Hariharan R., Lewenstein M., and Porat E. Overlap matching. Inform. and Comput. 181 1 (2003) 57-74
5. A. Amir, T. Hartman, O. Kapah, A. Levy, On the cost of interchange rearrangement in strings, manuscript
6. Amir A., Lewenstein M., and Porat E. Faster algorithms for string matching with k mismatches. J. Algorithms 50 2 (2004) 257-275
7. Bafna V., and Pevzner P.A. Sorting by transpositions. SIAM J. Discrete Math. 11 (1998) 221-240
8. B.S. Baker, A theory of parameterized pattern matching: Algorithms and applications, in: Proc. 25th Annual ACM Symposium on the Theory of Computation, 1993, pp. 71-80
9. Berman P., and Hannenhalli S. Fast sorting by reversal. In: Hirschberg D.S., and Myers E.W. (Eds). Proc. 8th Annual Symposium on Combinatorial Pattern Matching (CPM). Lecture Notes in Comput. Sci. vol. 1075 (1996), Springer-Verlag 168-185
10. Carpara A. Sorting by reversals is difficult. Proc. 1st Annual Intl. Conf. on Research in Computational Biology (RECOMB) (1997), ACM Press 75-83
11. Cayley A. Note on the theory of permutations. Philos. Mag. 34 (1849) 527-529
12. Christie D.A. Sorting by block-interchanges. Inform. Process. Lett. 60 (1996) 165-169
13. R. Cole, L.A. Gottlieb, M. Lewenstein, Dictionary matching and indexing with errors and don't cares, in: STOC '04: Proceedings of the Thirty-Sixth Annual ACM Symposium on Theory of Computing, 2004, pp. 91-100
14. R. Cole, R. Hariharan, Approximate string matching: A faster simpler algorithm, in: Proc. 9th ACM-SIAM Symposium on Discrete Algorithms (SODA) 1998, pp. 463-472
15. Diaconis P. Group Representations in Probability and Statistics (1988), IMS, Hayward, CA
16. Dvir Y. Covering properties of permutation groups. In: Arad Z., and Herzog M. (Eds). Products of Conjugacy Classes in Groups. Lecture Notes in Math. vol. 1112 (1985), Springer-Verlag, New York
17. P. Ferragina, R. Grossi, Fast incremental text editing, in: Proc. 7th ACM-SIAM Symposium on Discrete Algorithms, 1995, pp. 531-540
18. Fischer M.J., and Paterson M.S. String matching and other products. In: Karp R.M. (Ed). Complexity of Computation. SIAM-AMS Proc. vol. 7 (1974) 113-125
19. Galil Z., and Giancarlo R. Improved string matching with k mismatches. SIGACT News 17 4 (1986) 52-54
20. M. Gu, M. Farach, R. Beigel, An efficient algorithm for dynamic text indexing, in: Proc. 5th Annual ACM-SIAM Symposium on Discrete Algorithms, 1994, pp. 697-704
21. Karloff H. Fast algorithms for approximately counting mismatches. Inform. Process. Lett. 48 2 (1993) 53-60
22. Landau G.M., and Vishkin U. Efficient string matching with k mismatches. Theoret. Comput. Sci. 43 (1986) 239-249
23. Levenshtein V.I. Binary codes capable of correcting, deletions, insertions and reversals. Soviet Phys. Dokl. 10 (1966) 707-710
24. Lowrance R., and Wagner R.A. An extension of the string-to-string correction problem. J. ACM (1975) 177-183
25. Muthukrishnan S., and Ramesh H. String matching under a general matching relation. Inform. and Comput. 122 1 (1995) 140-148
26. S.C. Sahinalp, U. Vishkin, Efficient approximate and dynamic matching of patterns using a labeling paradigm, in: Proc. 37th FOCS, 1996, pp. 320-328
27. Schwartz J.T. Fast probabilistic algorithms for verification of polynomial identities. J. ACM 27 (1980) 701-717
28. Skiena S. Implementing Discrete Mathematics: Combinatorics and Graph Theory with Mathematica. ch. The Cycle Structure of Permutations, pp. 20-24 (1990), Addison-Wesley, MA
29. Vishne U. Mixing and covering in the symmetric group. J. Algebra 205 1 (1998) 119-140
30. A.C.C. Yao, Some complexity questions related to distributed computing, in: Proc. 11th Annual Symposium on the Theory of Computing (STOC) 1979, pp. 209-213
31. Zippel R. Probabilistic algorithms for sparse polynomials. Proc. EUROSAM. Lecture Notes in Comput. Sci. vol. 72 (1979), Springer-Verlag 216-226