Edit distance for genome comparison based on non-local operations

  • David Sankoff
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 644)


Detailed knowledge of gene maps and and even complete nucleotide sequences for small genomes has led to the feasibility of evolutionary inference based on the macrostructure of entire genomes, rather than on the traditional comparison of homologous versions of a single gene in different organisms. In this paper, we define a number of measures of gene order rearrangement, describe algorithm design and software development for the calculation of some of these quantities in single-chromosome genomes, and report on the the results of applying these tools to a database of mitochondrial gene orders inferred from genomic sequences.


Mitochondrial Genome Filamentous Fungus Fission Yeast Multicellular Organism Edit Distance 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Cedergren, R., Abel, Y. and Sankoff, D. (1991) in Molecular Techniques in Taxonomy (G. M. Hewitt, A.W.B. Johnston and J.P.W. Young, eds.) Springer-Verlag. 87–99.Google Scholar
  2. 2.
    Nadeau, J.H. and Taylor, B.A. (1984) Proceedings of the National Academy of Sciences USA 81, 814-8.Google Scholar
  3. 3.
    Palmer, J.D., Osorio, B. and Thompson, W.F. (1988) Current Genetics 14, 65–74.Google Scholar
  4. 4.
    Sankoff, D. (1989) Bulletin of the International Statistical Institute 47.3, 461–475Google Scholar
  5. 5.
    Sankoff, D., Cedergren, R. and Abel, Y. (1990) in Methods in Enzymology 183. Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, (R.F. Doolittle, ed.) Academic Press. 428–438.Google Scholar
  6. 6.
    Sankoff D. and Goldstein,M. (1988) Bulletin of Mathematical Biology 51, 117–124.Google Scholar
  7. 7.
    Sankoff, D., Kececioglu, J. and Leduc, G. (1992) manuscript in preparation.Google Scholar
  8. 8.
    Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., and Cedergren, R. (1992) Proceedings of the National Academy of Sciences USA to appear.Google Scholar
  9. 9.
    Sankoff, D, Leduc, G., and Rand, D. (1991) DERANGE. Minimum weight generation of oriented permutation by block inversions and block movements. Macintosh application, Centre de recherches mathématiques, Université de Montréal.Google Scholar
  10. 10.
    Watterson, G.A., Ewens, W.J., Hall, T.E. and Morgan, A. (1982) Journal of Theoretical Biology 99, 1–7.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1992

Authors and Affiliations

  • David Sankoff
    • 1
  1. 1.Centre de recherches mathématiquesUniversité de MontréalMontréal

Personalised recommendations