Some Open Problems in Computational Molecular Biology

Journal of Algorithms

Volumn 34, Issue 1, 2000, Pages 194-201

  Jiang, Tao ^a   Kearney, Paul ^b   Li, Ming ^b  

^a University of California Riverside   (United States)

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0013272768     PISSN: 01966774     EISSN: None     Source Type: Journal    
DOI: 10.1006/jagm.1999.1050     Document Type: Article

References (23)

1. V. Bafna, E. Lawler, and P. Pevzner, Approximation algorithms for multiple sequence alignment, Theoret. Comput. Sci. 182 (1997), 233-244.
2. V. Berry, T. Jiang, P. Kearney, M. Li, and T. Wareham, Quartet cleaning: Improved algorithms and simulations, in "Proc 7th Annual European Symposium on Algorithms, July, 1999, Prague, Czech Republic."
3. V. Berry, D. Bryant, T. Jiang, P. Kearney, M. Li, T. Wareham, and H. Zhang, A practical algorithm for recovering the best supported edges in an evolutionary tree, in, "Proc. 11th Annual ACM-SIAM Symp. on Discrete Algorithms, Jan, 2000," to appear.
4. P. Bonizzoni and G. Della Vedova, The complexity of multiple sequence alignment with SP-score that is metric, Theoret. Comput. Sci., in press.
5. P. Buneman, The recovery of trees from measures of dissimilarity, in "Mathematics in the Archaeological and Historical Sciences" (F. R. Hodson, D. G. Kendall, and P. Tautu, Eds.), pp. 387-395, Edinburgh University Press, Edinburgh, 1971.
6. D. Fasulo, T. Jiang, R. Karp, R. Settergren, and E. Thayer, An algorithmic approach to multiple complete digest mapping, J. Comput. Biol., in press.
7. M. R. Garey and D. S. Johnson, "Computers and Intractability: A Guide to the Theory of NP-Completeness," Freeman, New York, 1979.
8. D. Gusfield, Efficient methods for multiple sequence alignment with guaranteed error bounds, Bull. Math. Biol. 55 (1993), 141-154.
9. D. Gusfield, "Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology," Cambridge Univ. Press, Cambridge, UK, 1997.
10. S. L. Hakimi and S. S. Yau, Distance matrix of a graph and its realizability, Quart. Appl. Math. 22 (1964), 305-317.
11. T. Jiang and R. Karp, Mapping clones with a given ordering or interleaving, Algorithmica 21 (1998), 262-284.
12. T. Jiang, P. Kearney, and M. Li, Orchestrating quartets: approximation and data correction, in "Proc. 39th IEEE Symposium on Foundations of Computer Science, Palo Alto, CA, 1998."
13. W. Just, Reducing gap-0 multiple alignment to multiple alignment, manuscript, 1999.
14. S. Kannan and T. Warnow, Tree reconstruction from partial orders, SIAM J. Comput. 24 (1995), 511-519.
15. P. Kearney, R. B. Hayward, and H. Meijer, Inferring evolutionary trees from ordinal data, in "Proc. 8th Annual ACM-SIAM Symposium on Discrete Algorithms," 1997, pp. 418-426.
16. M. Li, B. Ma, and L. Wang, Finding similar regions in many sequences, in "Proc. 31st ACM Symp. Theory of Computing (STOC'99), 1999."
17. P. Pevzner, Multiple alignment, communication cost, and graph matching, SIAM J. Appl. Math. 56 (1992), 1763-1779.
18. J. Setubal and J. Meidanis, "Introduction to Computational Molecular Biology," PWS-Kent, Boston, 1997.
19. M. Steel, The complexity of reconstructing trees from qualitative characters and subtrees, J. Classification 9 (1992), 91-116.
20. L. Wang and T. Jiang, On the complexity of multiple sequence alignment, J. Comput. Biol. 1 (1994), 337-348.
21. M. Waterman, "Introduction to Computational Biology - Maps, Sequences and Genomes," Chapman & Hall, London/New York, 1995.
22. M. S. Waterman, T. F. Smith, M. Singh, and W. A. Beyer, Additive evolutionary trees, J. Theoret. Biol. 64 (1977), 199-213.
23. L. Zhang, personal communications.