software . 2021

FEVER Probe Design Algorithm

Kubicek-Sutherland, Jessica; Yusim, Karina; Theiler, James; Foley, Brian; Stromberg, Zachary; Gans, Jason;
Open Source
  • Published: 02 Jul 2021
  • Publisher: DOE CODE
Abstract
Here we have developed a pipeline for the fast evaluation of viral emerging risks (FEVER) that generates primer and probe sets for genetically diverse viruses. The goal of probe design is to produce a short nucleotide sequence (called a K-mer, as it is of length K) that reacts with SARS-CoV-2 without also reacting to background material that may be present in the sample that is being tested. Other desirable properties of the probe, making it more effective in the experimental setup, include maintaining a high G/C content and reducing the "hairpin propensity" (ie, the tendency of the probe string to fold over on itself) by ensuring that any self-complementary pai...
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