Skip to main content
SpringerLink
Log in

Constrained sequence alignment

  • Published:
Bulletin of Mathematical Biology Aims and scope Submit manuscript

Abstract

This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires onlyO(F) computation time andO(M+N) space, whereF is the area of the feasible region andM andN are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Literature

  • Altschul, S., W. Gish, W. Miller, E. W. Myers and D. Lipman. 1990. Basic local aligment search tool.J. molec. Biol. 215, 403–410.

    Article  Google Scholar 

  • Boguski, M., R. C. Hardison, S. Schwartz and W. Miller. 1992. 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 4, 247–260.

    Google Scholar 

  • Chao, K.-M., W. R. Pearson and W. Miller. 1992. Aligning two sequences within a aspecified diagonal band. To appear inCABIOS.

  • Chao, K.-M., and W. Miller. 1992. A sparse dynamic programming algorithm. Submitted.

  • Eppstein, D., Z. Galil, R. Giancarlo and G. F. Italiano. 1992. Sparse dynamic programming. I. Linear cost functions. To appear inJ. Assoc. Comput. Mach.

  • Galil, Z. and R. Giancarlo. 1989. Speeding up dynamic programming with applications to molecular biology.Theor. Comput. Sci. 64, 107–118.

    Article  MATH  MathSciNet  Google Scholar 

  • Hirschberg, D.S. 1975. A linear space algorithm for computing maximal common subsequences.Comm. ACM 18, 341–343.

    Article  MATH  MathSciNet  Google Scholar 

  • Huang, X., R. Hardison and W. Miller. 1990. A space-efficient algorithm for local similarities.CABIOS 6, 373–381.

    Google Scholar 

  • Huang, X. and W. Miller. 1991. A time-efficient, linear-space local similarity algorithm.Adv. appl. Math. 12, 337–357.

    Article  MATH  MathSciNet  Google Scholar 

  • Miller, W. and E. W. Myers. 1988. Sequence comparison with concave weighting functions.Bull. math. Biol. 50, 97–120.

    Article  MATH  MathSciNet  Google Scholar 

  • Myers, E. W. and W. Miller. 1988. Optimal alignments in linear space.CABIOS 4, 11–17.

    Google Scholar 

  • Myers, E. W. and W. Miller. 1989. Approximate matching of regular expressions.Bull. math. Biol. 51, 5–37.

    MATH  MathSciNet  Google Scholar 

  • Ohyama, K., H. Fukuzawa, T. Kohchi, H. Shirai, T. Sano, S. Sano, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S.-I. Aota, H. Inokuchi and H. Ozeki. 1986. Chloroplast gene organization deduced from complete sequence of liverwortMarchanta polymorpha chloroplast DNA.Nature 322, 572–574.

    Article  Google Scholar 

  • Palmer, J. 1991. Plastid chromosomes: structure and evolution. InThe Molecular Biology of Plastids. L. Bogorad and I. K. Vasil (Eds), Vol. 7,Cell Culture and Somatic Cell Genetics in Plants.

  • Rabani, Y. and Z. Galil. 1992. On the space complexity of some algorithms for sequence comparison.Theor. Comput. Sci. 95, 231–244.

    Article  MATH  MathSciNet  Google Scholar 

  • Schwartz, S., W. Miller, C.-M. Yang and R. C. Hardison. 1991. Software tools for analyzing pairwise alignments of long sequences.Nucl. Acids Res. 19, 4663–4667.

    Google Scholar 

  • Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayashi, N. Zaida, J. Chunwongse, J. Obokata, K. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusida, F. Takaiwa, A. Kato, N. Tohdoh, H. Shimada and M. Sugiura. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression.EMBO J. 5, 2043–2049.

    Google Scholar 

  • Shimada, H. and M. Sugiura. 1991. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes.Nucl. Acids Res. 19, 983–995.

    Google Scholar 

  • Waterman, M. S. 1984. Efficient sequence alignment algorithms.J. theor. Biol. 108, 333–337.

    MathSciNet  Google Scholar 

  • Wilbur, W. J. and D. J. Lipman. 1984. The context dependent comparison of biological sequences.SIAM J. appl. Math. 44, 557–567.

    Article  MATH  MathSciNet  Google Scholar 

  • Wolfe, K. H. and P. M. Sharp. 1988. Identification of functional open reading frames in chloroplast genomes.Gene 66, 215–222.

    Article  Google Scholar 

  • Zhou, D., O. Massenet, F. Quigley, M. Marion, P. Huber and R. Mache. 1988. Characterization of a large inversion in the spinach chloroplast genome relative to Marchantia: a possible transposon-mediated origin.Curr. Genet. 13, 433–439.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, The Pennsylvania State University, 16802, University Park, PA, U.S.A.

    Kun-Mao Chao & Webb Miller

  2. Department of Molecular and Cell Biology, The Pennsylvania State University, 16802, University Park, PA, U.S.A.

    Ross C. Hardison

  3. Institute for Molecular Evolutionary Genetics, The Pennsylvania State University, 16802, University Park, PA, U.S.A.

    Ross C. Hardison

Authors
  1. Kun-Mao Chao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ross C. Hardison
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Webb Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

K.-M. C. and W. M. were supported in part by grant R01 LM05110 from the National Library of Medicine. R. C. H. was supported by PHS grant R01 DK27635.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chao, KM., Hardison, R.C. & Miller, W. Constrained sequence alignment. Bltn Mathcal Biology 55, 503–524 (1993). https://doi.org/10.1007/BF02460648

Download citation

  • Received:

  • Revised:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02460648

Keywords

Search

Navigation