Published December 11, 2021 | Version v1.0.0
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DRM-labeled HIV-1 protease sequence dataset

Authors/Creators

  • 1. Scarsdale High School
  • 2. Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
  • 3. School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
  • 4. Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA; Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
  • 5. Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA

Description

An HIV-1 protease dataset with labeled DRMs derived from the Stanford HIV Drug Resistance Database1,2 is provided. It is in fasta format with major protease drug resistance mutations (as defined by Wensing et al.3) provided in the sequence name section (following the ">" symbol) as a comma-separated list. The dataset was used in the following paper: "Ahmed A., de Souza D. R., Link R. W., Nonnemacher M. R., Wigdahl B., Dampier W. Design of a SHERLOCK-based low resource screening assay for HIV-1 drug resistance, in preparation, 2021. "

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Additional details

References

  • Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 31(1), 298-303.
  • Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8
  • Wensing, A. M., Calvez, V., Ceccherini-Silberstein, F., Charpentier, C., Günthard, H. F., Paredes, R., Shafer, R. W., & Richman, D. D. (2019). 2019 update of the drug resistance mutations in HIV-1. Topics in antiviral medicine, 27(3), 111–121.
  • Ahmed, Armaan, De Souza, Diehl R., Link, Robert W., Nonnemacher, Michael R., Wigdahl, Brian, & Dampier, Will. (2021). Design of a SHERLOCK-based low resource screening assay for HIV-1 drug resistance. Discovery Day 2021, Philadelphia, PA, USA. Zenodo. https://doi.org/10.5281/zenodo.5719853