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Hepatitis C Virus Protocols pp 47–69Cite as

Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1911))

Abstract

The Virus Pathogen Resource (ViPR; www.viprbrc.org) is a US National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center providing bioinformatics support for major human viral pathogens. The hepatitis C virus (HCV) portal of ViPR facilitates basic research and development of diagnostics and therapeutics for HCV, by providing a comprehensive collection of HCV-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, and personal Workbench spaces for data storage and sharing. This chapter introduces the data and functionality provided by the ViPR HCV portal. It describes example workflows for (1) searching HCV genome and protein sequences, (2) conducting phylogenetic analysis, and (3) analyzing sequence variations using pattern search for amino acid substitutions in proteins, single nucleotide variation calculation, metadata-driven comparison, and sequence feature variant type analysis. All data and tools are freely available via the ViPR HCV portal at https://www.viprbrc.org/brc/home.spg?decorator=flavi_hcv.

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References

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Acknowledgment

This work was supported by the National Institutes of Health/National Institute for Allergy and Infectious Diseases [HHSN272201400028C].

Author information

Authors and Affiliations

  1. J. Craig Venter Institute, La Jolla, CA, USA

    Yun Zhang, Christian Zmasek & Richard H. Scheuermann

  2. Department of Pathology, University of California, San Diego, CA, USA

    Richard H. Scheuermann

  3. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA

    Richard H. Scheuermann

  4. Vecna Technologies, Greenbelt, MD, USA

    Guangyu Sun & Christopher N. Larsen

Authors
  1. Yun Zhang
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  2. Christian Zmasek
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  3. Guangyu Sun
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  4. Christopher N. Larsen
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  5. Richard H. Scheuermann
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Corresponding author

Correspondence to Richard H. Scheuermann .

Editor information

Editors and Affiliations

  1. Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA

    Mansun Law

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Zhang, Y., Zmasek, C., Sun, G., Larsen, C.N., Scheuermann, R.H. (2019). Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR). In: Law, M. (eds) Hepatitis C Virus Protocols . Methods in Molecular Biology, vol 1911. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8976-8_3

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  • DOI: https://doi.org/10.1007/978-1-4939-8976-8_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8975-1

  • Online ISBN: 978-1-4939-8976-8

  • eBook Packages: Springer Protocols

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