Skip to main content
SpringerLink
Log in
Book cover

International Workshop on Algorithms in Bioinformatics

WABI 2014: Algorithms in Bioinformatics pp 97–106Cite as

Linearization of Median Genomes under DCJ

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8701))

Abstract

Reconstruction of the median genome consisting of linear chromosomes from three given genomes is known to be intractable. There exist efficient methods for solving a relaxed version of this problem, where the median genome is allowed to have circular chromosomes. We propose a method for construction of an approximate solution to the original problem from a solution to the relaxed problem and prove a bound on its approximation accuracy. Our method also provides insights into the combinatorial structure of genome transformations with respect to appearance of circular chromosomes.

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. Sankoff, D., Cedergren, R.J., Lapalme, G.: Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA. Journal of Molecular Evolution 7(2), 133–149 (1976)

    Article  Google Scholar 

  2. Kováč, J., Brejová, B., Vinař, T.: A practical algorithm for ancestral rearrangement reconstruction. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS, vol. 6833, pp. 163–174. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  3. Gao, N., Yang, N., Tang, J.: Ancestral genome inference using a genetic algorithm approach. PLoS One 8(5), e62156 (2013)

    Google Scholar 

  4. Moret, B.M., Wyman, S., Bader, D.A., Warnow, T., Yan, M.: A New Implementation and Detailed Study of Breakpoint Analysis. In: Pacific Symposium on Biocomputing, vol. 6, pp. 583–594 (2001)

    Google Scholar 

  5. Bourque, G., Pevzner, P.A.: Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research 12(1), 26–36 (2002)

    Google Scholar 

  6. Caprara, A.: The reversal median problem. INFORMS Journal on Computing 15(1), 93–113 (2003)

    Article  MATH  MathSciNet  Google Scholar 

  7. Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10(1), 120 (2009)

    Article  Google Scholar 

  8. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)

    Article  Google Scholar 

  9. Alekseyev, M.A., Pevzner, P.A.: Multi-Break Rearrangements and Chromosomal Evolution. Theoretical Computer Science 395(2-3), 193–202 (2008)

    Article  MATH  MathSciNet  Google Scholar 

  10. Xu, A.W.: A fast and exact algorithm for the median of three problem: A graph decomposition approach. Journal of Computational Biology 16(10), 1369–1381 (2009)

    Article  MathSciNet  Google Scholar 

  11. Xu, A.W.: DCJ median problems on linear multichromosomal genomes: Graph representation and fast exact solutions. In: Ciccarelli, F.D., Miklós, I. (eds.) RECOMB-CG 2009. LNCS, vol. 5817, pp. 70–83. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  12. Zhang, M., Arndt, W., Tang, J.: An exact solver for the DCJ median problem. In: Pacific Symposium on Biocomputing, vol. 14, pp. 138–149 (2009)

    Google Scholar 

  13. Maňuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E.: Linearization of ancestral multichromosomal genomes. BMC Bioinformatics 13(suppl. 19), S11 (2012)

    Google Scholar 

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

    Article  Google Scholar 

  15. Muffato, M., Louis, A., Poisnel, C.-E., Crollius, H.R.: Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26(8), 1119–1121 (2010)

    Article  Google Scholar 

  16. Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Zhang, L., Miller, W., Haussler, D.: Dupcar: reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology 15(8), 1007–1027 (2008)

    Article  MathSciNet  Google Scholar 

  17. Alekseyev, M.A.: Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes. Journal of Computational Biology 15(8), 1117–1131 (2008)

    Article  MathSciNet  Google Scholar 

  18. Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences 65(3), 587–609 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  19. Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  20. Alekseyev, M.A., Pevzner, P.A.: Breakpoint graphs and ancestral genome reconstructions. Genome Research 19(5), 943–957 (2009)

    Article  Google Scholar 

  21. Jiang, S., Avdeyev, P., Hu, F., Alekseyev, M.A.: Reconstruction of ancestral genomes in presence of gene gain and loss (2014) (submitted)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Computational Biology Institute, The George Washington University, Ashburn, VA, U.S.A.

    Shuai Jiang & Max A. Alekseyev

Authors
  1. Shuai Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Max A. Alekseyev
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. David R. Cheriton School of Computer Science, University of Waterloo, ON, Canada

    Dan Brown

  2. Institute of Microbiology and Genetics, Department of Bioinformatics, University of Göttingen, Germany, Goldschmidtstr. 1, 37077, Göttingen, Germany

    Burkhard Morgenstern

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Jiang, S., Alekseyev, M.A. (2014). Linearization of Median Genomes under DCJ. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-44753-6_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-44752-9

  • Online ISBN: 978-3-662-44753-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation