Speeding Up Dynamic Programming without Omitting any Optimal Solution and Some Applications in Molecular Biology

Journal of Algorithms

Volumn 35, Issue 2, 2000, Pages 129-168

  Blum, Norbert ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0347307141     PISSN: 01966774     EISSN: None     Source Type: Journal    
DOI: 10.1006/jagm.2000.1078     Document Type: Article

References (22)

1. S. F. Altschul and B. W. Erickson, Optimal sequence alignment using affine gap costs, Bull. Math. Biol. 48 (1986), 603-616.
2. N. Blum, On locally optimal alignments in genetic sequences, in "9th STACS," 425-436, 1992.
3. H. N. Gabow and R. E. Tarjan, A linear-time algorithm for a special case of disjoint set union, J. Comput. System Sci. 30 (1985), 209-221.
4. Z. Galil and R. Giancarlo, Speeding up dynamic programming with applications to molecular biology, Theoret. Comput. Sci. 64 (1989), 107-118.
5. W. B. Goad and M. I. Kanehisa, Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries, Nuclear Acids Res. 10 (1982), 247-263.
6. O. Gotoh, An improved algorithm for matching biological sequences, J. Molec. Biol. 162 (1982), 705-708.
7. O. Gotoh, Optimal sequence alignment allowing for long gaps, Bull. Math. Biol. 52 (1990), 359-373.
8. X. Huang, A context dependent method for comparing sequences, in "5th CPM," pp. 54-63, 1994.
9. M. M. Klawe and D. J. Kleitman, An almost linear time algorithm for generalized matrix searching, SIAM J. Discrete Math. 3 (1990), 81-97.
10. W. Miller and E. W. Myers, Sequence comparison with concave weighting functions, Bull. Math. Biol. 50 (1988), 97-120.
11. D. Naor and D. L. Brutlag, On near-optimal alignments of biological sequences, J. Comput. Biol. 1 (1994), 349-366.
12. S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino-acid sequence of two-proteins, J. Molec. Biol. 48 (1970), 443-453.
13. P. H. Sellers, On the theory and computation of evolutionary distances, SIAM J. Appl. Math. 26 (1974), 787-793.
14. P. H. Sellers, The theory and computation of evolutionary distances: Pattern recognition, J. Algorithms 1 (1980), 359-373.
15. P. H. Sellers, Pattern recognition in genetic sequences by mismatch density, Bull. Math. Biol. 46 (1984), 501-514.
16. T. F. Smith and M. S. Waterman, Identification of common molecular subsequences, J. Molec. Biol. 147 (1981), 195-197.
17. J. E. Tarjan, "Data Structures and Network Algorithms," SIAM, Philadelphia, 1983.
18. M. S. Waterman, Efficient sequence alignment algorithms, J. Theoret. Biol. 108 (1984), 333-337.
19. M. S. Waterman, General methods of sequence comparison, Bull. Math. Biol. 46 (1984), 473-500.
20. M. S. Waterman, Sequence alignments, in "Mathematical Methods for DNA Sequences" (M. S. Waterman, Ed.), 53-92, CRC Press, Boca Raton, 1989.
21. M. S. Waterman and M. Eggert, A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons, J. Molec. Biol. 197 (1987), 723-728.
22. M. S. Waterman, T. F. Smith, and W. A. Beyer, Some biological sequence metrics, Adv. Math. 20 (1976), 367-387.