HCV quasispecies assembly using network flows

Kelly Westbrooks, Irina Astrovskaya, David Campo, Yury Khudyakov, Piotr Berman, Alex Zelikovsky

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    28 Scopus citations

    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.

    Original languageEnglish (US)
    Title of host publicationBioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings
    Pages159-170
    Number of pages12
    DOIs
    StatePublished - Aug 27 2008
    Event4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008 - Atlanta, GA, United States
    Duration: May 6 2008May 9 2008

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume4983 LNBI
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008
    CountryUnited States
    CityAtlanta, GA
    Period5/6/085/9/08

    All Science Journal Classification (ASJC) codes

    • Theoretical Computer Science
    • Computer Science(all)

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  • Cite this

    Westbrooks, K., Astrovskaya, I., Campo, D., Khudyakov, Y., Berman, P., & Zelikovsky, A. (2008). HCV quasispecies assembly using network flows. In Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings (pp. 159-170). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4983 LNBI). https://doi.org/10.1007/978-3-540-79450-9_15