Skip to main content
SpringerLink
Log in

Towards a computational theory of genome rearrangements

  • Chapter
  • First Online:
Computer Science Today

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1000))

Abstract

Analysis of genome rearrangements in molecular biology started in the late 1930's, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions for the species of Drosophila. However, until recently there were no computer science results allowing a biologist to analyze genome rearrangements. The paper describes combinatorial problems motivated by genome rearrangements, surveys recently developed algorithms for genomic sequence comparison and presents applications of these algorithms to analyze rearrangements in herpes viruses, plant organelles, and mammalian chromosomes.

This work is supported by NSF Young Investigator Award, NSF grant CCR-9308567, NIH grant 1R01 HG00987 and DOE grant DE-FG02-94ER61919.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. M. Aigner and D. B. West. Sorting by insertion of leading element. Journal of Combinatorial Theory, 45:306–309, 1987.

    Article  Google Scholar 

  2. N. Amato, M. Blum, S. Irani, and R. Rubinfeld. Reversing trains: A turn of the century sorting problem. Journal of Algorithms, 10:413–428, 1989.

    Article  Google Scholar 

  3. V. Bafna and P. Pevzner. Genome rearrangements and sorting by reversals. In 34th Annual IEEE Symposium on Foundations of Computer Science, pages 148–157, 1993. (to appear in SIAM J. Computing).

    Google Scholar 

  4. V. Bafna and P. Pevzner. Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome. Mol. Biol. and Evol., 12:239–246, 1995a.

    Google Scholar 

  5. V. Bafna and P. Pevzner. Sorting by transpositions. In Proc. 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 614–623, 1995b.

    Google Scholar 

  6. E. Boudreau. 1995 (personal communication).

    Google Scholar 

  7. E. Boudreau, C. Otis, and M. Turmel. Conserved gene clusters in the highly rearranged chloroplast genomes of chlamydomonas moewusii and chlamydomonas reinhardtii. Plant Molecular Biology, 24:585–602, 1994.

    Article  PubMed  Google Scholar 

  8. N. G. Copeland, N. A. Jenkins, D. J. Gilbert, J. T. Eppig, L. J. Maltals, J. C. Miller, W. F. Dietrich, A. Weaver, S. E. Lincoln, R. G. Steen, L. D. Steen, J. H. Nadeau, and E. S. Lander. A genetic linkage map of the mouse: Current applications and future prospects. Science, 262:57–65, 1993.

    PubMed  Google Scholar 

  9. M. Davisson. X-linked genetic homologies between mouse and man. Genomics, 1:213–227, 1987.

    Article  PubMed  Google Scholar 

  10. S. Even and O. Goldreich. The minimum-length generator sequence problem is NP-hard. Journal of Algorithms, 2:311–313, 1981.

    Article  Google Scholar 

  11. C. Fauron and M. Havlik. The maize mitochondrial genome of the normal type and the cytoplasmic male sterile type T have very different organization. Current Genetics, 15:149–154, 1989.

    Article  Google Scholar 

  12. W. H. Gates and C. H. Papadimitriou. Bounds for sorting by prefix reversals. Discrete Mathematics, 27:47–57, 1979.

    Article  Google Scholar 

  13. E. Györi and E. Turan. Stack of pancakes. Studia Sci. Math. Hungar., 13:133–137, 1978.

    Google Scholar 

  14. S. Hannenhalli. Polynomial algorithm for computing translocation distance between genomes. In Combinatorial Pattern Matching, Proc. 6th Annual Symposium (CPM'95), Lecture Notes in Computer Science, pages 162–176. Springer-Verlag, Berlin, 1995.

    Google Scholar 

  15. S. Hannenhalli, C. Chappey, E. Koonin, and P. Pevzner. Scenarios for genome rearrangements: Herpesvirus evolution as a test case. In Proc. 3rd Intl. Conference on Bioinformatics and Complex Genome Analysis, pages 91–106, 1995.

    Google Scholar 

  16. S. Hannenhalli and P. Pevzner. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In Proc. 27th Annual ACM Symposium on the Theory of Computing, 1995a. (to appear).

    Google Scholar 

  17. S. Hannenhalli and P. Pevzner. To cut... or not to cut (applications of comparative physical maps in molecular evolution). Technical Report: CSE-94-074, Department of Computer Science and Engineering, The Pennsylvania State University, 1995b.

    Google Scholar 

  18. S. Hannenhalli and P. Pevzner. Transforming men into mice (polynomial algorithm for genomic distance problem). In 36th Annual IEEE Symposium on Foundations of Computer Science, 1995c. (to appear).

    Google Scholar 

  19. R. J. Hoffmann, J. L. Boore, and W. M. Brown. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics, 131:397–412, 1992.

    Google Scholar 

  20. S. B. Hoot and J. D. Palmer. Structural rearrangements including parallel inversions within the chloroplast genome of anemone and related genera. Journal of Molecular Evolution, 38:274–281, 1994.

    Article  PubMed  Google Scholar 

  21. A. Jauch, J. Wienberg, Stanyon, N. Arnold, S. Tofanelli, T. Ishida, and T. Cremer. Reconstruction of genomic rearrangements in great apes gibbons by chromosome painting. Proc. Natl. Acad. Sci., 89:8611–8615, 1992.

    PubMed  Google Scholar 

  22. M. Jerrum. The complexity of finding minimum-length generator sequences. Theoretical Computer Science, 36:265–289, 1985.

    Article  Google Scholar 

  23. J. Kececioglu and R. Ravi. Of mice and men: Evolutionary distances between genomes under translocation. In Proc. 6th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 604–613, 1995.

    Google Scholar 

  24. J. Kececioglu and D. Sankoff. Exact and approximation algorithms for the inversion distance between two permutations. In Combinatorial Pattern Matching, Proc. 4th Annual Symposium (CPM'93), volume 684 of Lecture Notes in Computer Science, pages 87–105. Springer-Verlag, Berlin, 1993. (Extended version has appeared in Algorithmica, 13: 180–210, 1995.).

    Google Scholar 

  25. J. Kececioglu and D. Sankoff. Efficient bounds for oriented chromosome inversion distance. In Combinatorial Pattern Matching, Proc. 5th Annual Symposium (CPM'94), volume 807 of Lecture Notes in Computer Science 807, pages 307–325. Springer-Verlag, Berlin, 1994.

    Google Scholar 

  26. E. V. Koonin and V. V. Dolja. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Molec. Biol., 28:375–430, 1993.

    Google Scholar 

  27. M. F. Lyon. X-Chromosome Inactivation and the Location and Expression of X-linked Genes. Am. J. Hum. Genet, 42:008–016, 1988.

    Google Scholar 

  28. J. H. Nadeau and B. A. Taylor. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA, 81:814–818, 1984.

    PubMed  Google Scholar 

  29. S. O'Brien and J. Graves. Report of the committee on comparative gene mapping in mammals. Cytogenet. Cell Genet., 58:1124–1151, 1991.

    Google Scholar 

  30. S. Ohno. Sex chromosomes and sex-linked genes. Springer, Heidelberg, 1967.

    Google Scholar 

  31. J. D. Palmer and L. A. Herbon. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution, 27:87–97, 1988.

    Article  Google Scholar 

  32. P.A. Pevzner and M.S. Waterman. Open combinatorial problems in computational molecular biology. In 3rd Israel Symposium on Theory of Computing and Systems, pages 158–163. IEEE Computer Society Press, 1995.

    Google Scholar 

  33. L. A. Raubeson and R. K. Jansen. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255:1697–1699, 1992.

    Google Scholar 

  34. G. Rettenberger, C. Klett, U. Zechner, J. Kunz, W. Vogel, and H. Hameister. Visualization of the conservation of synteny between humans and pigs by hetereologous chromosomal painting. Genomics, 26:372–378, 1995.

    Article  PubMed  Google Scholar 

  35. D. Sankoff. Edit distance for genome comparison based on non-local operations. In Combinatorial Pattern Matching, Proc. 3rd Annual Symposium (CPM'92), volume 644 of Lecture Notes in Computer Science, pages 121–135. Springer-Verlag, Berlin, 1992.

    Google Scholar 

  36. D. Sankoff, R. Cedergren, and Y. Abel. Genomic divergence through gene rearrangement. In Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, chapter 26, pages 428–438. Academic Press, 1990.

    Google Scholar 

  37. 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. Proc. Natl. Acad. Sci. USA, 89:6575–6579, 1992.

    PubMed  Google Scholar 

  38. H. Scherthan, T. Cremer, U. Arnason, H. Weier, A. Lima de Faria, and L. Fronicke. Comparative chromosomal painting discloses homologous segments in distantly related mammals. Nature Genetics, 6:342–347, April 1994.

    Article  PubMed  Google Scholar 

  39. A. H. Sturtevant and T. Dobzhansky. Inversions in the third chromosome of wild races of drosophila pseudoobscura, and their use in the study of the history of the species. Proc. Nat. Acad. Sci., 22:448–450, 1936.

    Google Scholar 

  40. G. A. Watterson, W. J. Ewens, T. E. Hall, and A. Morgan. The chromosome inversion problem. Journal of Theoretical Biology, 99:1–7, 1982.

    Article  Google Scholar 

  41. J. Whiting, M. Pliley, J. Farmer, and D. Jeffery. In situ hybridization analysis of chromosomal homologies in Drosophila melanogaster and Drosophila virilis. Genetics, 122:99–109, 1989.

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, The Pennsylvania State University, 16802, University Park, PA

    Sridhar Hannenhalli & Pavel A. Pevzner

  2. Institute for Molecular Evolutionary Genetics, The Pennsylvania State University, 16802, University Park, PA

    Pavel A. Pevzner

Authors
  1. Sridhar Hannenhalli
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pavel A. Pevzner
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Jan van Leeuwen

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Hannenhalli, S., Pevzner, P.A. (1995). Towards a computational theory of genome rearrangements. In: van Leeuwen, J. (eds) Computer Science Today. Lecture Notes in Computer Science, vol 1000. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0015244

Download citation

  • DOI: https://doi.org/10.1007/BFb0015244

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-60105-0

  • Online ISBN: 978-3-540-49435-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation