Skip to main content
SpringerLink
Log in
Book cover

RECOMB International Workshop on Comparative Genomics

RECOMB-CG 2010: Comparative Genomics pp 252–263Cite as

Consistency of Sequence-Based Gene Clusters

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6398))

Abstract

In comparative genomics, various combinatorial models can be used to specify gene clusters — groups of genes that are co-located in a set of genomes. Several approaches have been proposed to reconstruct putative ancestral gene clusters based on the gene order of contemporary species. One prevalent and natural reconstruction criterion is consistency: For a set of reconstructed gene clusters, there should exist a gene order that comprises all given clusters.

In this paper, we discuss the consistency problem for different gene cluster models on sequences with restricted gene multiplicities. Our results range from linear-time algorithms for the simple model of adjacencies to NP completeness for more complex models like common intervals.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adam, Z., Turmel, M., Lemieux, C., Sankoff, D.: Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution. J. Comp. Biol. 14(4), 436–445 (2007)

    Article  CAS  Google Scholar 

  2. Bergeron, A., Blanchette, M., Chateau, A., Chauve, C.: Reconstructing ancestral gene order using conserved intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 14–25. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  3. Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. J. Comp. Biol. 13(7), 1340–1354 (2006)

    Article  CAS  Google Scholar 

  4. Bhutkar, A., Gelbart, W.M., Smith, T.F.: Inferring genome-scale rearrangement phylogeny and ancestral gene order: A drosophila case study. Genome Biol. 8(11), R236 (2007)

    Google Scholar 

  5. Blin, G., Stoye, J.: Finding nested common intervals efficiently. J. Comp. Biol. (to appear 2010); A preliminary version appeared in Proc. of RECOMB-CG 2009. LNCS (LNBI), vol. 5817, pp. 59–69 (2009)

    Google Scholar 

  6. Böcker, S., Jahn, K., Mixtacki, J., Stoye, J.: Computation of median gene clusters. J. Comp. Biol. 16(8), 1085–1099 (2009)

    Article  Google Scholar 

  7. Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4(11), e1000234 (2008)

    Google Scholar 

  8. Csűrös, M., Miklós, I.: Mathematical framework for phylogenetic birth-and-death models. Arxiv preprint arXiv:0902.0970 (2009)

    Google Scholar 

  9. Hoberman, R., Durand, D.: The Incompatible Desiderata of Gene Cluster Properties. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 73–87. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  10. Hsu, W.-L., McConnell, R.: PQ-trees, PC-trees, and planar graphs. In: Mehta, D.P., Sahni, S. (eds.) Handbook of Data Structures and Applications (2004)

    Google Scholar 

  11. Huynen, M.A., Snel, B., Bork, P.: Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17(6), 304–306 (2001)

    Article  CAS  PubMed  Google Scholar 

  12. Itai, A., Papadimitriou, C.H., Szwarcfiter, J.L.: Hamilton paths in grid graphs. SIAM J. Computing 11(4), 676–686 (1982)

    Article  Google Scholar 

  13. Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., et al.: Genome duplication in the teleost fish tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431(7011), 946–957 (2004)

    Article  PubMed  Google Scholar 

  14. Lawrence, J.G., Roth, J.R.: Selfish operons: Horizontal transfer drive the evolution of gene clusters. Genetics 143(4), 1843–1860 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, J.W., Blanchette, M., Haussler, D., Miller, W.Z.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16(12), 1557–1565 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Overbeek, R., Fonstein, M., D’Souza, M., Pusch, G.D., Maltsev, N.: The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96(6), 2896–2901 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Page, R.D.M., Charleston, M.A.: From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phyl. and Evol. 7(2), 231–240 (1997)

    Article  CAS  Google Scholar 

  18. Rahmann, S., Klau, G.W.: Integer linear programs for discovering approximate gene clusters. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 298–306. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  19. Stoye, J., Wittler, R.: A unified approach for reconstructing ancient gene clusters. IEEE/ACM Trans. Comput. Biol. Bioinf. 6(3), 387–400 (2009)

    Article  Google Scholar 

  20. Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290–309 (2000)

    Article  Google Scholar 

  21. Wittler, R.: Phylogeny-based Analysis of Gene Clusters. Ph.D. Thesis, Faculty of Technology, Bielefeld University (2010), http://bieson.ub.uni-bielefeld.de/volltexte/2010/1627/

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics, Simon Fraser University, Burnaby, (BC), Canada

    Roland Wittler & Jens Stoye

  2. Technische Fakultät, Universität Bielefeld, Germany

    Roland Wittler

Authors
  1. Roland Wittler
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jens Stoye
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. INRIA Rhône-Alpes, Université de Lyon 1, Villeurbanne, France

    Eric Tannier

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Wittler, R., Stoye, J. (2010). Consistency of Sequence-Based Gene Clusters. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_21

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-16181-0_21

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16180-3

  • Online ISBN: 978-3-642-16181-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation