A polynomial-time approximation scheme for minimum routing cost spanning trees

SIAM Journal on Computing

Volumn 29, Issue 3, 2000, Pages 761-778

  Wu, Bang Ye ^a   Lancia, Giuseppe ^b   Bafna, Vineet ^c   Chao, Kun Mao ^d   Ravi, R ^e   Tang, Chuan Yi ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF PADOVA   (Italy)

^c CELERA GENOMICS   (United States)

^d PROVIDENCE UNIVERSITY   (Taiwan)

^e CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

Approximation algorithms; Computational biology; Network design; Spanning trees

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; GRAPH THEORY; POLYNOMIALS; TREES (MATHEMATICS);

COMPUTATIONAL BIOLOGY; MINIMUM ROUTING; POLYNOMIAL TIME APPROXIMATION; SPANNING TREES;

APPROXIMATION THEORY;

EID: 0033293966     PISSN: 00975397     EISSN: None     Source Type: Journal    
DOI: 10.1137/S009753979732253X     Document Type: Article

References (22)

1. R. K. AHUJA, T. L. MAGNANTI, AND J. B. ORLIN, Network Flows - Theory, Algorithms, and Applications, Prentice-Hall, Englewood Cliffs, NJ, 1993.
2. V. BAFNA, E. L. LAWLER, AND P. PEVZNER, Approximation algorithms for multiple sequence alignment, Proceedings of the 5th Combinatorial Pattern Matching Conference, Lecture Notes in Comput. Sci. 807, Springer, New York, 1994, pp. 43-53.
3. Y. BARTAL, Probabilistic approximation of metric spaces and its algorithmic applications, Proceedings of the 37th Annual IEEE Symposium on Foundations of Computer Science, Burlington, VT, 1996, pp. 184-193.
4. Y. BARTAL, On approximating arbitrary metrics by tree metrics, Proceedings of the 30th Annual ACM Symposium on Theory of Computing, Dallas, TX, 1998, pp. 161-168.
5. H. CARRILLO AND D. LIPMAN, The multiple sequence alignment problem in biology, SIAM J. Appl. Math., 48 (1988), pp. 1073-1082.
6. M. CHARIKAR, C. CHEKURI, A. GOEL, AND S. GUHA, Rounding via trees: Deterministic approximation algorithms for group Steiner trees and k-median, Proceedings of the 30th Annual ACM Symposium on Theory of Computing, Dallas, TX, 1998, pp. 114-123.
7. T. H. CORMEN, C. E. LEISERSON, AND R. L. RIVEST, Introduction to Algorithms, MIT Press, Cambridge, MA, 1994.
8. D. FENG AND R. DOOLITTLE, Progressive sequence alignment as a prerequisite to correct phylogenetic trees, J. Molecular Evol., 25 (1987), pp. 351-360.
9. D. GUSFIELD, Efficient methods for multiple sequence alignment with guaranteed error bounds, Bull. Math. Biology, 55 (1993), pp. 141-154.
10. T. C. HU, Optimum communication spanning trees, SIAM J. Comput., 3 (1974), pp. 188-195.
11. D. S. JOHNSON, J. K. LENSTRA, AND A. H. G. RINNOOY KAN, The complexity of the network design problem, Networks, 8 (1978), pp. 279-285.
12. G. KONJEVOD, R. RAVI, AND F. S. SALMAN, On Approximating Planar Metrics by Tree Metrics, manuscript, 1997.
13. D. J. LIPMAN, S. F. ALTSCHUL, AND J. D. KECECIOGLU, A tool for multiple sequence alignment, Proc. Nat. Acad. Sci. USA, 86 (1989), pp. 4412-4415.
14. S. B. NEEDLEMAN AND C. D. WUNSCH, A general method applicable to search the similarities in the amino acid sequences of two proteins, J. Molecular Biol., 48 (1970), pp. 443-453.
15. P. A. PEVZNER, Multiple alignment, communication cost, and graph matching, SIAM J. Appl. Math., 52 (1992), pp. 1763-1779.
16. Y. RABINOVICH AND R. RAZ, Lower bounds on the distortion of embedding finite metric spaces in graphs, Discrete Comput. Geom., 19 (1998), pp. 79-94.
17. D. SANKOFF AND J. B. KRUSKAL, eds. Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley, Reading, MA, 1983.
18. D. SANKOFF, C. MOREL, AND R. J. CEDERGREN, Evolution of the 55 Ribosomal RNA, Nature New Biology, 245 (1973), pp. 232-234.
19. G. D. SCHULER, S. F. ALTSCHUL, AND D. J. LIPMAN, A workbench for multiple alignment construction and analysis, Proteins Structure Function Genetics, 9 (1991), pp. 180-190.
20. L. WANG AND T. JIANG, On the complexity of multiple sequence alignment, J. Comput. Biol., 1 (1994), pp. 337-348.
21. M. S. WATERMAN, Introduction to Computational Biology, Chapman & Hall, London, 1995.
22. R. WONG, Worst-case analysis of network design problem heuristics, SIAM J. Alg. Discrete Methods, 1 (1980), pp. 51-63.