This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Dynamic Programming Alignment of Sequences Representing Cyclic Patterns
February 1993 (vol. 15 no. 2)
pp. 129-135

String alignment by dynamic programming is generalized to include cyclic shift and corresponding optimal alignment cost for strings representing cyclic patterns. A guided search algorithm uses bounds on alignment costs to find all optimal cyclic shifts. The bounds are derived from submatrices of an initial dynamic programming matrix. Algorithmic complexity is analyzed for major stages in the search. The applicability of the method is illustrated with satellite DNA sequences and circularly permuted protein sequences.

[1] H. Bunke and A. Sanfelieu, Eds.Syntactic and Structural Pattern Recognition Theory and Applications. Singapore: World Scientific, 1990.
[2] M. Carlson and D. Brutlag, "Different regions of a complex satellite DNA vary in size and sequence of the repeating unit,"J. Molecular Biol., vol. 135, pp. 483-500, 1979.
[3] B. A. Cunningham, J. F. Hemperly, T. P. Hopp, and G. M. Edelman, "Favin versus concanavalin A: Circularly permuted amino acid sequences," inProc. Nat. Acad. Sci., 1979, pp. 3218-3222, vol. 76.
[4] B. W. Erickson and P. H. Sellers, "Recognition of patterns in genetic sequences," in D. Sankoff and J. B. Kruskal,Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparisons. Reading, MA: Addison-Wesley, 1983, pp. 55-90.
[5] K. S. Fu and S. Y. Lu, "Size normalization and pattern orientation problems in syntactic clustering,"IEEE Trans. Syst. Man Cybern., vol. 9, pp. 55-58, 1979.
[6] T. Hsieh and D. Brutlag, "Sequence and sequence variation within the 1.688 g/cm3satellite DNA ofdrosophila melanogaster," J. Molecular Biol., vol. 135, pp. 465-481, 1979.
[7] M. Maes, "On a cyclic string-to-string correction problem,"Inform. Processing Lett., vol. 35, pp. 73-78, 1990.
[8] D. Sankoff and J. B. Kruskal, Eds.Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparisons. Reading, MA: Addison-Wesley, 1983.
[9] P. H. Sellers, "An algorithm for the distance between two finite sequences,"J. Combinatoric Theory, vol. A16, pp. 253-258, 1974.
[10] W. -H. Tsai and S. -S. Yu, "Attributed string matching with merging for shape recognition,"IEEE Trans. Patt. Anal. Machine Intell., vol. PAMI-7, pp. 453-462, 1985.
[11] R. Wagner and M. Fischer, "The string-to-string correction problem,"J. ACM, vol. 21, pp. 168-173, 1974.
[12] Y. P. Wang and T. Pavlidis, "Optimal correspondence of string subsequences,"IEEE Trans. Patt. Anal. Machine Intell., vol. 12, pp. 1080-1087, 1990.

Index Terms:
algorithmic complexity; cyclic patterns; dynamic programming; optimal alignment cost; guided search algorithm; alignment costs; submatrices; satellite DNA sequences; circularly permuted protein sequences; dynamic programming; image sequences; medical image processing
Citation:
J. Gregor, M.G. Thomason, "Dynamic Programming Alignment of Sequences Representing Cyclic Patterns," IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 15, no. 2, pp. 129-135, Feb. 1993, doi:10.1109/34.192484
Usage of this product signifies your acceptance of the Terms of Use.