Advertisement

On the Nadeau-Taylor theory of conserved chromosome segments

  • David Sankoff
  • Marie-Noelle Parent
  • Isabelle Marchand
  • Vincent Ferretti
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1264)

Abstract

The quantification of comparative genomics dates from 1984 with the work of Nadeau and Taylor on estimating interchromosomal exchange rates based on the rearrangement of chromosomal segments in human versus mouse genomes. We reformulate their analysis in terms of a probabilistic model based on spatial homogeneity and independence of breakpoints and gene distribution. We study the marginal distribution of the number of genes per segment and the distribution of the number of non-empty segments as a function of the number of genes and segments. We propose a rapid algorithm for identifying a given number of conserved segments in noisy comparative map data. Finally, we propose a model which incorporates a degree of in-homogeneity in the distribution of genes and/or breakpoints. Comparative maps of human and mouse genomes serve as test data throughout.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    W. Feller. An Introduction to Probability Theory and its Applications, Vol. 1. 3d ed. New York: John Wiley and Son, 1968.Google Scholar
  2. 2.
    I. Marchand. Generalisations du modèle de Nadeau et Taylor sur les segments chromosomiques conservés. MSc thesis, Departement de mathématiques et de statistique, Université de Montréal. 1997.Google Scholar
  3. 3.
    J.H. Nadeau and B. A. Taylor Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences USA, 81: 814–818, 1984.Google Scholar
  4. 4.
    M.-N. Parent. Estimation du nombre de segments vides dans le modèle de Nadeau et Taylor sur les segments chromosomiques conservés. MSc thesis, Département de mathématiques et de statistique, Université de Montréal. 1997.Google Scholar
  5. 5.
    D. Sankoff and V. Ferretti. Karotype distributions in a stochastic model of reciprocal ranslocation. Genome Research 6, 1–9, 1996.Google Scholar
  6. 6.
    D. Sankoff, V. Ferretti and J.H. Nadeau. Conserved segment identification. RECOMB 97. Proceedings of the First Annual International Conference on Computational Molecular Biology. New York: ACM Press, 1997, pp. 252–256.Google Scholar
  7. 7.
    D. Sankoff and J.H. Nadeau. Conserved synteny as a measure of genomic distance. Discrete Applied Mathematics 71, 247–257, 1996.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1997

Authors and Affiliations

  • David Sankoff
    • 1
  • Marie-Noelle Parent
    • 1
  • Isabelle Marchand
    • 1
  • Vincent Ferretti
    • 1
  1. 1.Centre de recherches mathématiquesUniversité de MontréalMontréal

Personalised recommendations