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Original Synteny

  • Vincent Ferretti
  • Joseph H. Nadeau
  • David Sankoff
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1075)

Abstract

The inference of genome rearrangement requires detailed gene maps of related species. For most multichromosomal species, however, knowledge of chromosomal assignment of genes outstrips mapping data. Comparison of these species is thus a question of comparing sets of syntenic genes, without any gene order or gene orientation information. Given synteny data from present-day species, can we infer the synteny sets of ancestor species? How many chromosomes did these ancestors possess, and what genes were on each one? We first study the problem of calculating a syntenic edit distance between two genomes, based on reciprocal translocation, chromosome fusion and fission. This distance is then used in the analysis of the median problem for synteny, and hence for a prelimary approach to phylogenetic inference of synteny.

Keywords

Genome Rearrangement Phylogenetic Inference Reciprocal Translocation Internal Vertex Terminal Vertex 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    S. Hannenhalli and P.A. Pevzner. Transforming cabbage into turnip. (polynomial algorithm for sorting signed permutations by reversals). Proceedings of the 36th Annual Symposium on Foundations of Computer Science, 1995.Google Scholar
  2. 2.
    J. Kececioglu and D. Sankoff. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica, 13:180–210, 1995.Google Scholar
  3. 3.
    D. Sankoff, R.J. Cedergren, and G. Lapalme. Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA. Journal of Molecular Evolution, 7:133–149, 1976.PubMedGoogle Scholar
  4. 4.
    D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B.F. Lang, and R. Cedergren. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences USA 89, 6575–6579, 1992.Google Scholar
  5. 5.
    I. A. Zakharov. Measurements of similarity of synteny groups and an analysis of genome rearrangements in the evolution of mammals. In Bioinformatics, supercomputing and complex genome analysis, H. Lim, J. Fickett and C. Cantor (eds), World Scientific, 1993.Google Scholar
  6. 6.
    B. Das Gupta, T. Jiang, S. Kannan, M. Li, and Z. Sweedyk. Personal communication, March 1996.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1996

Authors and Affiliations

  • Vincent Ferretti
    • 1
  • Joseph H. Nadeau
    • 2
    • 3
  • David Sankoff
    • 1
  1. 1.Centre de recherches mathématiquesUniversité de MontréalMontréal
  2. 2.Department of Human Genetics, Montreal General HospitalMcGill UniversityMontréal
  3. 3.Jackson LaboratoryBar Harbor

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