Abstract
Comparative genetic maps between two species which position genes on chromosomes allow syntenic blocks of one or more genes to be identified. These may then be used, with appropriate models, to estimate the number of chromosomal segments with conserved content between species. We outline a model for the distribution of the lengths of unobserved segments on each chromosome which allows for widely differing chromosome lengths. The model is motivated by, and applied to data from two comparative maps for the chicken, one with human and one with mouse. The performance of two genome based models is also compared for these maps, and for simulations based upon them.
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References
Andersson, L., Ashburner, M., Audun, S., Barendse, W., Bitgood, J. J., et al. 1996. Mammalian genome. In Comparative Genome Organization of Vertebrates: The First International Workshop on Comparative Genome Organization, volume 7, pp. 717–734.
Burt, D. W., Bruley, C., Dunn, I. C., Jones, C. T., Ramage, A., Law, A. S., Morrice, D. R., Paton, I. R., Smith, J., Windsor, D., Sazanov, A., Fries, R., and Waddington, D. 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402:411–413.
Burt, D. W., Bumstead, N., Bltgood, J. J., Ponce De Leon, F. A., and Crit-Tenden, L. B. 1995. Chicken genome mapping: a new era in avian genetics. Trends in Genetics 11:190–194.
Carver, E. A. and Stubbs, L. 1997. Zooming in on the human-mouse comparative map: genome conservation re-examined on a high-resolution scale. Genome Research 94:1123–1137.
Collett, D. 1991. Modelling binary data. Chapman and Hall, London.
Lyness, J. N. 1983. When not to use an automated quadrature routine. SIAM Review 25:63–87.
Nadeau, J. H. and Sankoff, D. 1998. Counting on comparative maps. Trends in Genetics 14:495–501.
Nadeau, J. H. and Taylor, B. A. 1984. Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences USA 81:814–818.
Plackett, R. L. 1971. An Introduction to the Theory of Statistics. Oliver and Boyd, Edinburgh.
Sankoff, D. 1999. Comparative mapping and genome rearrangement. In J. C. M. Dekkers, S. J. Lamont, and M. F. Rothschild (eds.), From Jay L. Lush to Genomics: Visions for Animal Breeding and Genetics, pp. 124–134. Iowa State University, Ames, Iowa.
Sankoff, D., Ferretti, V., and Nadeau, J. H. 1997a. Conserved segment identification. Journal of Computational Biology 559:559–565.
Sankoff, D. and Nadeau, J. H. 1996. Conserved synteny as a measure of genomic distance. Discrete Applied Mathematics 71:247–257.
Sankoff, D., Parent, M.-N., Marchand, I., and Ferretti, V. 1997b. On the Nadeau-Taylor theory of conserved chromosome segments. In A. Apostolico and Hein (eds.), Combinational Pattern Matching, 8th Annual Symposium, Lecture Notes in Computer Science, pp. 262–274, New York. Springer-Verlag.
Schoen, D. J. 2000. Comparative genomics, marker density and statistical analysis of chromosome rearrangements. Genetics 154:943–952.
Waddington, D., Springbett, A. J., and Burt, D. 2000. A chromosome based model for estimating the number of conserved segments between pairs of species from comparative genetic maps. Genetics 154:323–332.
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© 2000 Springer Science+Business Media Dordrecht
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Waddington, D. (2000). Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model. In: Sankoff, D., Nadeau, J.H. (eds) Comparative Genomics. Computational Biology, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4309-7_29
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DOI: https://doi.org/10.1007/978-94-011-4309-7_29
Publisher Name: Springer, Dordrecht
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