A Heuristic Algorithm for Multiple Sequence Alignment Based on Blocks

Journal of Combinatorial Optimization

Volumn 5, Issue 1, 2001, Pages 95-115

  Zhao, Peng ^a   Jiang, Tao ^b  

^a IBM TORONTO LAB   (Canada)

^b University of California Riverside   (United States)

Author keywords

Block chaining; Conserved blocks; Multiple sequence alignment

Indexed keywords

EID: 0043285300     PISSN: 13826905     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1009841718561     Document Type: Article

References (25)

1. A.V. Aho, J.E. Hopcroft, and J.D. Ullman, Data Structures and Algorithms, Addison-Wesley: Reading, Massachusetts, 1985, pp. 163-169.
2. G.J. Barton and M.J.E. Sternberg, "Evaluation and improvements in automatic alignment of protein sequences," Protein Eng., vol. 1, pp. 89-94, 1987a.
3. G.J. Barton and M J.E. Sternberg, "A strategy for the rapid multiple alignment of protein sequences confidence levels from tertiary structure comparisons," J. Mol. Biol., vol. 198, pp. 327-337, 1987b.
4. M. Boguski, R.C. Hardison, S. Schwarts, and W. Miller, "Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization," The New Biologist, vol. 4, pp. 247-260, 1992.
5. A. Brazma, I. Jonassen, I. Eidhammer, and D. Gilbert, "Approaches to the automatic discovery of patterns in biosequences," Technical report, Department of Informatics, University of Bergen, 1995.
6. K.-M. Chao and W. Miller, "Linear-space algorithms that build local alignments from fragments," Algorithmica, vol. 13, pp. 106-134, 1995.
7. T.H. Cormen, C.E. Leiserson, and R.L. Rivest, Introduction to Algorithms, The MIT Press: Cambridge, Massachusetts, 1990.
8. D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, "Sparse dynamic programming. I: linear cost functions," J. Assoc. Comput. Mach., vol. 39, pp. 519-545, 1992a.
9. D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, "Sparse dynamic programming. II: convex and concave cost functions," J. Assoc. Comput. Mach., vol. 39, pp. 546-567, 1992b.
10. D.E. Feng and R.F. Doolittle, "Progressive sequence alignment as a prerequisite to correct phylogenetic trees," J. Mol. Evol., vol. 25, pp. 351-360, 1987.
11. D.S. Johnson, "Approximation algorithms for combinatorial problems," J. Comput. System Sci., vol. 7, pp. 256-278, 1974.
12. D.J. Lipman, S.F. Altschul, and J.D. Kececioglu, "A tool for multiple sequence alignment," Proc. Natl. Acad. Sci. USA, vol. 86, pp. 4412-4415, 1989.
13. D. Maier, "The complexity of some problems on subsequences and supersequences," J. ACM, pp. 322-336, 1978.
14. M.A. McClure, T.K. Vasi, and W.M. Fitch, "Comparative analysis of multiple protein-sequence alignment methods," Mol. Biol. Evol., vol. 11, no. 4, pp. 571-592, 1994.
15. W. Miller, "Building multiple alignments from pairwise alignments," CABIOS, vol. 9, pp. 169-176, 1993.
16. W. Miller, M. Boguski, B. Raghavachari, Z. Zhang, and R.C. Hardison, "Constructing aligned sequence blocks," J. Computat. Biol., vol. 1, no. 1, pp. 51-64, 1994.
17. B. Morgenstern, A. Dress, and T. Werner, "Multiple DNA and protein sequence alignment based on segment-to-segment comparison," Proc. Nat. Acad. Sci. USA, vol. 93, pp. 12098-12103, 1996.
18. L. Parida, A. Floratos, and I. Rigoutsos, "An approximation algorithm for alignment of multiple sequences using motif discovery," J. Combinatorial Optimization, vol. 20, no. 7, 1999.
19. E. Sobel and H.M. Martinez, "A multiple sequence alignment program," Nucl. Acids Res., vol. 14, no. 1, pp. 363-374, 1986.
20. J. Thompson, D. Higgins, and T. Gibson, "CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Necleic Acids Res., vol. 22, pp. 4673-4680, 1994.
21. S. Tsukiyama, M. Ide, H. Ariyoshi, and I. Shirakawa, "A new algorithm for generating all the maximal independent sets," SIAM J. Comput., vol. 6, pp. 505-517, 1977.
22. L. Wang and T. Jiang, "On the complexity of multiple sequence alignment," J. Computat. Biol., vol. 1, no. 4, pp. 337-348, 1994.
23. M.S. Waterman and R. Jones, "Consensus methods for DNA and protein sequence alignment," Methods in Enzymology, vol. 183, pp. 221-237, 1990.
24. Z. Zhang, B. He, and W Miller, "Local multiple alignment via subgraph enumeration," Discreet Appl. Math., vol. 71, pp. 337-365, 1996.
25. Z. Zhang, B. Raghavachari, R.C. Hardison, and W Miller, "Chaining multiple-alignment blocks," J. Computat. Biol., vol. 1, no. 3, pp. 217-226, 1994.