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

Part of the Methods in Molecular Biology book series (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.

Key words

  • Virus Pathogen Resource
  • ViPR
  • Database
  • Annotation
  • Genotype
  • Mature peptides
  • Comparative genomics
  • Phylogenetics
  • Antiviral
  • Drug resistance

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  • DOI: 10.1007/978-1-4939-8976-8_3
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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].

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Correspondence to Richard H. Scheuermann .

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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

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