Multiple sequence alignment as a facility-location problem

INFORMS Journal on Computing

Volumn 16, Issue 4, 2004, Pages 430-440

  Just, Winfried ^a   Delia Vedova, Gianluca ^b  

^a OHIO UNIVERSITY   (United States)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

Analysis of algorithms: Computational complexity; Facilities equipment planning: Location

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; DATA ACQUISITION; DNA; POLYNOMIALS; PROBLEM SOLVING; PROTEINS;

BIOLOGICAL DATA; FACILITY-LOCATION PROBLEM; MULTIPLE SEQUENCE ALIGNMENT; POLYNOMIAL-TIME APPROXIMATION SCHEME (PTAS);

MOLECULAR BIOLOGY;

EID: 10044249891     PISSN: 10919856     EISSN: 15265528     Source Type: Journal    
DOI: 10.1287/ijoc.1040.0093     Document Type: Article

References (25)

1. Alimonti, P., V. Kann. 1997. Hardness of approximating problems on cubic graphs. Italian Conf. Algorithms Complexity 97, Lecture Notes in Computer Science, No. 1203, Springer Verlag, Berlin, Germany, 288-298.
2. Arkin, E. M., M. Hassin. 2000. Minimum diameter covering problems. Networks 36 147-155.
3. Arora, S., D. Karger, M. Karpinski. 1999. Polynomial time approximation schemes for dense instances of NP-hard problems. J. Comput. Systems Sci. 58 193-210.
4. Bafna, V., E. L. Lawler, P. A. Pevzner. 1997. Approximation algorithms for multiple sequence alignment. Theoret. Comput. Sci. 182 233-244.
5. Benner, S. A., M. A. Cohen, G. H. Gonnet. 1993. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Molecular Dial. 229 1065-1082.
6. Bonizzoni, P., G. Delia Vedova. 2001. The complexity of multiple alignment with SP-score that is a metric. Theoret. Comput. Sci. 259 63-79.
7. Chvátal, V., D. Sankoff. 1983. An upper-bound technique for lengths of common subsequences. D. Sankoff, J. B. Kruskal, eds. Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparisons, Chapter 15. Addison Wesley, Boston, MA.
8. Elias, I. 2003. Settling the intractability of multiple alignment. Internat. Sympos. Algorithms Comput., Lecture Notes in Computer Science, No. 2906, Springer-Verlag, Berlin, Germany, 352-363.
9. Fitch, W. M. 1993. Letter to the editor: Commentary on the letter by Ward C. Wheeler. Molecular Biol. Evolution 10 713-714.
10. Garey, M. R., D. S. Johnson. 1979. Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, New York.
11. Garg, N., G. Konjevod, R. Ravi. 2000. A polylogarithmic approximation algorithm for the group Steiner tree problem. J. Algorithms 37 66-84.
12. Gusfield, D. 1993. Efficient methods for multiple sequence alignment with guaranteed error bounds. Bull Math. Biol. 55 141-154.
13. Jiang, T., P. Kearney, M. Li. 1999. Some open problems in computational molecular biology. SIGACT News 30 43-49.
14. Just, W. 2001. Computational complexity of multiple sequence alignment with SP-score. J. Comput. Biol. 8 615-623.
15. Just, W., G. Della Vedova. 2000. Multiple Sequence Alignment as a Facility Location Problem. M. Balik, M. Simanek, eds. Proc. Prague Stringology Club Workshop 2000. Collaborative report DC-2000-03. Department of Computer Science and Engineering, Czech Technical University, Prague, 60-70.
16. Li, M., B. Ma, L. Wang. 2002. Finding similar regions in many strings. J. Comput. Systems Sci. 65 73-96.
17. Manthey, B. 2003. Non-approximability of weighted multiple sequence alignment. Theoret. Comput. Sci. 296 179-192.
18. Pascarella, S., P. Argos. 1992. Analysis of insertions/deletions in protein structures. J. Molecular Biol. 224 461-471.
19. Pevzner, P. A. 1992. Multiple alignment, communication cost, and graph matchings. SIAM J. Appl. Math. 52 1763-1779.
20. Sankoff, D., J. B. Kruskal. 1983. Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparisons. Addison Wesley, Boston, MA.
21. Tamir, A. 1994. A distance constrained p-facility location problem on the real line. Math. Programming 66 201-204.
22. Wang, L., T. Jiang. 1994. On the complexity of multiple sequence alignment. J. Comput. Biol. 1 337-348.
23. Wareham, H. T. 1995. A simplified proof of the NP- and MAX SNP-hardness of multiple sequence tree alignment. J. Comput. Biol. 2 509-514.
24. Wheeler, W. C. 1993. Letter to the editor: The triangle inequality and character analysis. Molecular Biol. Evolution 10 707-712.
25. Wu, B. Y., G. Lancia, V. Bafna, K.-M. Chao, R. Ravi, C. Y. Tang. 1999. A polynomial-time approximation scheme for minimum routing cost spanning trees. SIAM J. Comput. 29 761-778.