Skip to main content
SpringerLink
Log in

Probabilistic models of genome shuffling

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

Abstract

The comparison of entire genomes in evolutionary studies gives rise to alignments characterized by many intersections, or inversions in the order of two fragments in different genomes. To model this, we suggest a random migration process for fragments, and discuss its equilibrium distribution in the case of linear and circular genomes. Simulations are carried out to explore “cut-off” behavior as the process approaches equilibrium. We define a new process to take into account the indistinguishability of two fragments which are adjacent in both genomes being compared. Questions of applicability of these models are discussed.

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

References

  • Aldous, D. and P. Diaconis. 1986. “Shuffling Cards and Stopping Times.”Am. Math. Mont. 93, 333–348.

    Article  MATH  MathSciNet  Google Scholar 

  • — and —. 1987. “Strong Uniform Times and Random Walks.”Adv. Appl. Math. 8, 69–97.

    Article  MATH  MathSciNet  Google Scholar 

  • Feller, W. 1957.An Introduction to Probability Theory and Its Applications. New York: Wiley.

    Google Scholar 

  • Kruskal, J. B. and D. Sankoff. 1983. “An Anthology of Algorithms and Concepts for Sequence Comparison.”Time Warps String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison, D. Sankoff and J. B. Kruskal (Eds), pp. 265–310.

  • Logan, B. F. and L. A. Shepp. 1977. “A Variational Problem for Young Tableux.”Adv. Math. 26, 206–222.

    Article  MATH  MathSciNet  Google Scholar 

  • Lowrance, R. and R. A. Wagner. 1975. “An Extension of the String-to-String Correction Problem”.J. Assoc. Comput. Mach. 22, 177–183.

    MATH  MathSciNet  Google Scholar 

  • Wagner, R. A. 1983. “On the Complexity of the Extended String-to-String Correction Problem.”Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison, D. Sankoff and J. B. Kruskal (Eds), pp. 215–235.

Download references

Author information

Authors and Affiliations

  1. Centre de recherches mathématiques and Department de mathématiques et statistique, Université de Montréal, Succursale “A”, C.P.6128, H3C 3J7, Montréal, Canada

    David Sankoff & Martin Goldstein

Authors
  1. David Sankoff
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin Goldstein
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sankoff, D., Goldstein, M. Probabilistic models of genome shuffling. Bltn Mathcal Biology 51, 117–124 (1989). https://doi.org/10.1007/BF02458839

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02458839

Keywords

Search

Navigation