Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 3, Issue 4, 2006, Pages 408-422

  Bilu, Yonatan ^a   Agarwal, Pankaj K ^b   Kolodny, Rachel ^c  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b Duke University   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Algorithms; Dynamic programming; Multiple sequence alignment; Shortest path

Indexed keywords

MULTIPLE SEQUENCE ALIGNMENT; OPTIMAL SOLUTION; SHORTEST PATH;

COMPUTATIONAL COMPLEXITY; DYNAMIC PROGRAMMING; GRAPH THEORY; HEURISTIC METHODS; MOLECULAR BIOLOGY; PROBLEM SOLVING;

ALGORITHMS;

ALGORITHM; ARTICLE; BASE MISPAIRING; CHROMOSOME MAP; DNA SEQUENCE; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TRANSPOSON;

ALGORITHMS; BASE PAIR MISMATCH; CHROMOSOME MAPPING; DNA TRANSPOSABLE ELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 33845609285     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2006.53     Document Type: Conference Paper

References (43)

1. S. Altschul, F. Stephen, L.M. Thomas, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman, "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs," Nucleic Acids Research, vol. 25, pp. 3389-3402, 1997.
2. A. Bairoch and R. Apweiler, "The SWISS-PROT Protein Sequence Data Bank and Its Supplement TrEMBL," Nucleic Acids Research, vol.25, no. 1, pp. 31-36, 1997.
3. P. Bunizzoni and G. Della Vedova, "The Complexity of Multiple Sequence Alignment with Sp-Score that Is a Metric," Theoretical Computer Science, vol. 259, nos. 1-2, pp. 63-79, 2001.
4. H. Carrillo and D. Lipman, "The Multiple Sequence Alignment Problem in Biology," SIAM J. Applied Math., vol. 48, no. 5, pp. 1073-1082, 1988.
5. F. Corpet, "Multiple Sequence Alignment with Hierarchical- Clustering," Nucleic Acids Research, vol. 16, no. 22, pp. 10881-10890, 1988.
6. C.B. Do, M.A. Mahabhashyam, M. Brudno, and S. Batzoglou, "ProbCons: Probabilistic Consistency-Based Multiple Sequence Alignment," Genome Research, vol. 15, no. 2, pp. 330-340, 2005.
7. R.G. Downey and M. Fellows, Parameterized Complexity. Springer-Verlag, 1999.
8. R.C. Edgar, "MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput," Nucleic Acids Research, vol. 32, no. 5, pp. 1792-1797, 2004.
9. R.C. Edgar, "MUSCLE: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity," BMC Bioinformatics, vol. 5, p. 113, 2004.
10. I. Elias, "Settling the Intractability of Multiple Alignment," Proc. Ann. Jnt'l Symp. 'Algorithms and Computation (ISAAC), pp. 352-363, 2003.
11. D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, "Sparse Dynamic-Programming: I. Linear Cost-Functions," J. ACM, vol. 39, no. 3, pp. 519-545, 1992.
12. D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, "Sparse Dynamic-Programming: II. Convex and Concave Cost-Functions," J. ACM, vol. 39, no. 3, pp. 546-567, 1992.
13. D.F. Feng and R.F. Doolittle, "Progressive Sequence Alignment as a Prerequisite to Correct Phylogenetic Trees," J. Molecular Evolution, vol. 25, pp. 351-360, 1987.
14. M.R. Garey and D.S. Johnson, Computers and Intractability - A Guide to the Theory of NP-Completeness. Freeman, 1979.
15. D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge Univ. Press, 1997.
16. S. Henikoff and J.G. Henikoff, "Amino Acid Substitution Matrices from Protein Blocks," Proc. Nat'l Academy of Sciences, vol. 89, pp. 10915-10919, 1992.
17. D.G. Higgins and P.M. Sharp, "Clustal - A Package for Performing Multiple Sequence Alignment on a Microcomputer," Gene, vol. 73, no. 1, pp. 237-244, 1988.
18. T. Jiang and L. Wang, "On the Complexity of Multiple Sequence Alignment," J. Computer Biology, vol. 1, no. 4, pp. 337-348, 1994.
19. W. Just, "Computational. Complexity of Multiple Sequence Alignment with Sp-Score," J. Computer Biology, vol. 8, no. 6, pp. 615-623, 2001.
20. G.M. Landau, M. Crochemore, and M. Ziv-Ukelson, "A Subquadratic Sequence Alignment Algorithm for Unrestricted Cost Matrices," Proc. 13th Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 679-688, 2002.
21. T. Lassmann and E.L.L. Sonnhammer, "Quality Assessment of Multiple Alignment Programs," Febs Letters, vol. 529, no. 1, pp. 126-130, 2002.
22. C. Lee, C. Grasso, and M.F. Sharlow, "Multiple Sequence Alignment Using Partial Order Graphs," Bioinformatics, vol. 18, no. 3, pp. 452-464, 2002.
23. M. Lermen and K. Reinert, "The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment," J. Computer Biology, vol. 7, no. 5, pp. 655-672, 2000.
24. H.P. Lenhof, B. Morgenstern, and K. Reinert, "An Exact Solution for the Segment-to-Segment Multiple Sequence Alignment Problem," Bioinformatics, vol. 15, no. 3, pp. 203-210, 1999.
25. B. Manthey, "Non-Approximability of Weighted Multiple Sequence Alignment," Theoretical Computer Science, vol. 296, no. 1, pp. 179-192, 2003.
26. W.J. Masek and M.S. Paterson, "A Faster Algorithm Computing String Edit Distances," J. Computer Systems Science, vol. 20, no. 1, pp. 18-31, 1980.
27. B. Morgenstern, "Dialign 2: Improvement of the Segment-to-Segment Approach to Multiple Sequence Alignment," Bioinformatics, vol. 15, no. 3, pp. 211-218, 1999.
28. B. Morgenstern, "A Simple and Space-Efficient Fragment-Chaining Algorithm for Alignment of DNA and Protein Sequences," Applied Math. Letters, vol. 15, no. 1, pp. 11-16, 2002.
29. B. Morgenstern, A. Dress, and T. Werner, "Multiple DNA and Protein Sequence Alignment Based on Segment-to-Segment Comparison," Proc. Nat'l Academy of Sciences, vol. 93, no. 22, pp. 12098-12103, 1996.
30. M. Murata, J.S. Richardson, and J.L. Sussman, "Simultaneous Comparison of 3 Protein Sequences," Proc. Nat'l Academy of Science, vol. 82, no. 10, pp. 3073-3077, 1985.
31. G. Myers and W. Miller, "Chaining Multiple-Alignment Fragments in Subquadratic Time," Proc. Sixth Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 38-47, 1995.
32. S.B. Needleman and C.D. Wunsch, "A General Method Applicable to the Search for Similarities in the Amino Acid Sequences of Two Proteins," J. Molecular Biology, vol. 48, pp. 443-453, 1970.
33. C. Notredame, "Recent Progress in Multiple Sequence Alignment: A Survey," Pharmacogenomics, vol. 3, no. 1, pp. 131-144, 2002.
34. C. Notredame, D.G. Higgins, and J. Heringa, "T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment," J. Molecular Biology, vol.. 302, no. 1, pp. 205-217, 2000.
35. G.D. Schuler, S.F.F. Altschul, and D.J. Lipman, "A Workbench for Multiple Alignment Construction and Analysis," Proteins-Structure Function and Genetics, vol. 9, no. 3, pp. 180-190, 1991.
36. R.M. Schwartz and M.O. Dayhoff, "Matrices for Detecting Distant Relationships," Atlas of Protein Sequences and Structure, pp. 353-358, 1979.
37. T.F. Smith and M.S. Waterman, "Comparison of Biosequences," Advanced Applied Math., vol. 2, no. 4, pp. 482-489, 1981.
38. S.-H. Sze, Y. Lu, and Q. Yang, "A Polynomial Time Solvable Formulation of Multiple Sequence Alignment," J. Computational Biology, to appear.
39. J.D. Thompson, D.G. Higgins, and T.J. Gibson, "Clustal-W - Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice," Nucleic Acids Research, vol. 22, no. 22, pp. 4673-4680, 1994.
40. J.D. Thompson, F. Plewniak, and O. Poch, "BAliBASE: A Benchmark Alignment Database for the Evaluation of Multiple Alignment Programs," Bioinformatics, vol. 15, pp. 87-88, 1999.
41. W.J. Wilbur and D.J. Lipman, "Rapid Similarity Searches of Nucleic-Acid and Protein Data Banks," Proc. Nat'l Academy of Sciences, vol. 80, no. 3, pp. 726-730, 1983.
42. W.J. Wilbur and D.J. Lipman, "The Context Dependent Comparison of Biological Sequences," SLAM J. Applied Math., vol. 44, no. 3, pp. 557-567, 1984.
43. H. Zhou and Y. Zhou, "SPEM: Improving Multiple Sequence Alignment with Sequence Profiles and Predicted Secondary Structures," Bioinformatics, vol. 21, no. 18, pp. 3615-3621, 2005.