Publications

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

Li K, Shrivastava S, Brownley A, Katzel D, Bera J, Nguyen AT, Thovarai V, Halpin R, Stockwell TB

PMID: 23131097

Abstract

In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally.