Skip to main content

HCV Quasispecies Assembly Using Network Flows

  • Conference paper
Bioinformatics Research and Applications (ISBRA 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4983))

Included in the following conference series:

Abstract

Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. By exploiting knowledge of the forces that guide viral microevolution, researchers can design drugs and treatments that are effective against newly evolved strains. Therefore, it is critical to develop a method for typing the genomes of all of the variants of a virus (quasispecies) inside an infected individual cell.

In this paper, we focus on sequence assembly of Hepatitis C Virus (HCV) based on 454 Lifesciences system that produces around 250K reads each 100-400 base long. We introduce several formulations of the quasispecies assembly problem and a measure of the assembly quality. We also propose a novel scalable assembling method for quasispecies based on a novel network flow formulation. Finally, we report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of HCV.

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

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Von Hahn, T., Yoon, J.C., Alter, H., Rice, C.M., Rehermann, B., Balfe, P., Mckeating, J.A.: Hepatitis C Virus Continuously Escapes From Neutralizing Antibody and T-Cell Responses During Chronic Infection In Vivo. Gastroenterology 132, 667–678 (2007)

    Article  Google Scholar 

  2. Myers, G.: Building Fragment Assembly String Graphs. In: European Conf. on Computational Biology, pp. 79–85 (2005)

    Google Scholar 

  3. Lippert, R., Schwartz, R., Lancia, G., Istrail, S.: Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics 3(1), 23–31 (2002)

    Article  Google Scholar 

  4. Alekseyev, M.A., Pevzner, P.A.: Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Trans Comput Biol Bioinform. 4(1), 98–107

    Google Scholar 

  5. Chaisson, M.J., Pevzner, P.A.: Short read fragment assembly of bacterial genomes. Genome research (to appear, 2007)

    Google Scholar 

  6. Sundquist, A., Ronaghi, M., Tang, H., Pevzner, P., Batzoglou, S.: Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS ONE 2(5), e484 (2007)

    Article  Google Scholar 

  7. Brinza, D., Zelikovsky, A.: 2SNP: Scalable Phasing Based on 2-SNP Haplotypes. Bioinformatics 22(3), 371–373 (2006)

    Article  Google Scholar 

  8. 454 Lifescience (2007), http://www.454.com/

  9. Margulies, M., et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057), 376–380 (2005)

    Google Scholar 

  10. Albert, R., DasGupta, B., Dondi, R., Sontag, E., Zelikovsky, A., Westbrooks, K.: Signal Transduction Network Inference from Indirect Experimental Evidence. Journal of Computational Biology 14(7), 927–949 (2007)

    Article  MathSciNet  Google Scholar 

  11. Goldberg, A.: An Effcient Implementation of a Scaling Minimum-Cost Flow Algorithm. Journal of Algorithms 22(1), 1–29 (1997)

    Article  MathSciNet  Google Scholar 

  12. GNU Linear Programming Kit, http://www.gnu.org/software/glpk/

  13. ILOG CPLEX, http://www.ilog.com/products/cplex/

  14. IG Systems CS2 Software (2007), http://www.igsystems.com/cs2/

  15. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., et al.: Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Ion Măndoiu Raj Sunderraman Alexander Zelikovsky

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Westbrooks, K., Astrovskaya, I., Campo, D., Khudyakov, Y., Berman, P., Zelikovsky, A. (2008). HCV Quasispecies Assembly Using Network Flows. In: Măndoiu, I., Sunderraman, R., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2008. Lecture Notes in Computer Science(), vol 4983. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-79450-9_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-79450-9_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-79449-3

  • Online ISBN: 978-3-540-79450-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics