Parametric multiple sequence alignment and phylogeny construction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1848, Issue , 2000, Pages 69-83

  Fernández Baca, David ^a   Seppäläinen, Timo ^b   Slutzki, Giora ^a  

^a Iowa State University   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY;

MULTIPLE SEQUENCE ALIGNMENTS; PARAMETER SPACE DECOMPOSITIONS; PHYLOGENETIC INFORMATION; PHYLOGENY CONSTRUCTIONS;

PATTERN MATCHING;

EID: 84868003442     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45123-4_8     Document Type: Conference Paper

References (36)

1. Pankaj K. Agarwal and Micha Sharir. Davenport-Schinzel Sequences and their Geometric Applications. Cambridge University Press, Cambridge-New York- Melbourne, 1995.
2. Stephen F. Altschul. Gap costs for multiple sequence alignment. J. Theor. Biol., 138:297-309, 1989.
3. Stephen F. Altschul. Leaf pairs and tree dissections. SIAM J. Disc. Math., 2(3):293-299, 1989.
4. Stephen F. Altschul, Raymond J. Carrol, and David J. Lipman. Weights for data related by a tree. J. Mol. Biol., 207:647-653, 1989.
5. Stephen F. Altschul and David J. Lipman. Trees, stars, and multiple biological sequence alignment. SIAM J. Appl. Math., 49(1):197-209, 1989.
6. M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, 5:345-352, 1978.
7. David Dobkin, Herbert Edelsbrunner, and C. K. Yap. Probing convex polytopes. In Proceedings of the 18th Annual ACM Symposium on Theory of Computing, pages 424-432, 1986.
8. David Dobkin, Herbert Edelsbrunner, and C. K. Yap. Probing convex polytopes. In Cox and Wilfong, editors, Autonomous Robot Vehicles, pages 328-341. Springer-Verlag, 1990.
9. Herbert Edelsbrunner. Algorithms in Combinatorial Geometry. Springer-Verlag, Heidelberg, 1987.
10. M.J. Eisner and D.G. Severance. Mathematical techniques for efficient record segmentation in large shared databases. J. Assoc. Comput. Mach., 23:619-635, 1976.
11. J. Felsenstein. Phylogeny programs. http://evolution.genetics.washington.edu/phylip/software.html.
12. D. Feng and R.F. Doolittle. Progressive alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25:351-360, 1987.
13. David Fernáandez-Baca, Timo Seppäläinen, and Giora Slutzki. Bounds for parametric sequence comparison. In Proc. Symp. on String Processing and Information Retrieval, pages 55-62. IEEE Computer Society, 1999.
14. David Fernández-Baca and S. Srinivasan. Constructing the minimization diagram of a two-parameter problem. Operations Research Letters, 10:87-93, 1991.
15. S. K. Gupta, J. Kececioglu, and A. A. Schäffer. Improving the practical space and time eficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. Journal of Computational Biology, 2:459-472, 1995.
16. Dan Gusfield. Sensitivity analysis for combinatorial optimization. Technical Report UCB/ERL M80/22, University of California, Berkeley, May 1980.
17. Dan Gusfield. Parametric combinatorial computing and a problem in program module allocation. J. Assoc. Comput. Mach., 30(3):551-563, 1983.
18. Dan Gusfield. Eficient algorithms for multiple sequence alignment with guaranteed error bounds. Bull. Math. Biol., 55:141-154, 1993.
19. Dan Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge-New York- Melbourne, 1997.
20. Dan Gusfield, K. Balasubramanian, and Dalit Naor. Parametric optimization of sequence alignment. Algorithmica, 12:312-326, 1994.
21. Dan Gusfield and Robert W. Irving. Parametric stable marriage and minimum cuts. Information Processing Letters, 30:255-259, 1989.
22. Dan Gusfield and Paul Stelling. Parametric and inverse-parametric sequence alignment with XPARAL. In Russell F. Doolittle, editor, Computer methods for macro- molecular sequence analysis, volume 266 of Methods in Enzymology, pages 481-494. Academic Press, 1996.
23. S. Henikoff and J.G. Henikoff. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89:10915-10919, 1992.
24. Xiaoqiu Huang, Pavel A. Pevzner, and Webb Miller. Parametric recomputing in alignment graphs. In M. Crochemore and D. Gusfield, editors, Combinatorial Pattern Matching, volume 807 of Lecture Notes in Computer Science, pages 87-101. Springer-Verlag, 1994.
25. T. Jiang and L. Wang. On the complexity of multiple sequence alignment. Journal of Computational Biology, 1:337-348, 1994.
26. Tao Jiang, Eugene L. Lawler, and Lusheng Wang. Aligning sequences via an evolutionary tree: Complexity and approximation (extended abstract). In Proc. 26th Ann. Symp. Theory of Computing, pages 760-769, 1994.
27. D. J. Lipman, S. F. Altschul, and J. D. Kececioglu. A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA, 86:4412-4415, 1989.
28. Franco P. Preparata and Michael Ian Shamos. Computational Geometry: An In- troduction. Springer-Verlag, 1985.
29. D. Sankoff and R. J. Cedergren. Simultaneous comparison of three or more sequences related by a tree. In Sankoff and Kruskal [31], pages 253-263.
30. David Sankoff. Minimal mutation trees of sequences. SIAM J. Appl. Math., 28(1):35-42, January 1975.
31. David Sankoff and Joseph B. Kruskal, editors. Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison- Wesley, Reading, MA, 1983.
32. Tetsuo Shibuya and Hiroshi Imai. New flexible approaches for multiple sequence alignment. Journal of Computational Biology, 4(3):385-413, 1997.
33. Martin Vingron. Sequence alignment and phylogeny construction. In M. Farach-Colton et al., editor, Mathematical Support for Molecular Biology, volume 47 of DI- MACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1998.
34. Martin Vingron and Michael S.Waterman. Sequence alignment and penalty choice: Review of concepts, case studies, and implications. J. Mol. Biol., 235:1-12, 1994.
35. Michael S. Waterman, M. Eggert, and Eric Lander. Parametric sequence comparisons. Proc. Natl. Acad. Sci. USA, 89:6090-6093, 1992.
36. Ward C. Wheeler. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Bio., 44(3):321-331, 1995.