Virus Quasispecies Assembly using Network Flows
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Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. In this talk I focus on optimization problems in sequence assembly for viruses based on 454 Lifesciences system. Several formulations of the quasispecies assembly problem and a measure of the assembly quality will be given. I will describe a scalable assembling method for quasispecies based on network flow and maximum likelihood formulations and then give details of existing and novel methods for reliably assembling quasipsecies that have very long common segments. Finally, I report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of Hepatitis C Virus.