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HCV Quasispecies Assembly Using Network Flows

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Bioinformatics Research and Applications (ISBRA 2008)

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

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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.

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Ion Măndoiu Raj Sunderraman Alexander Zelikovsky

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© 2008 Springer-Verlag Berlin Heidelberg

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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.

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  • 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)

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