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Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis

Part of the Methods in Molecular Biology book series (MIMB,volume 1604)

Abstract

During the last decade, genome sequence-based classification of viruses has become increasingly prominent. Viruses can be even classified based on coding-complete genome sequence data alone. Nevertheless, classification remains arduous as experts are required to establish phylogenetic trees to depict the evolutionary relationships of such sequences for preliminary taxonomic placement. Pairwise sequence comparison (PASC) of genomes is one of several novel methods for establishing relationships among viruses. This method, provided by the US National Center for Biotechnology Information as an open-access tool, circumvents phylogenetics, and yet PASC results are often in agreement with those of phylogenetic analyses. Computationally inexpensive, PASC can be easily performed by non-taxonomists. Here we describe how to use the PASC tool for the preliminary classification of novel viral hemorrhagic fever-causing viruses.

Key words

  • Pairwise sequence comparison analysis
  • PASC
  • Species demarcation
  • VHF
  • Viral hemorrhagic fever
  • Virus classification
  • Virus taxonomy

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Acknowledgments

We thank Vyacheslav Chetvernin for developing and maintaining the PASC tool. We also thank Laura Bollinger of the IRF-Frederick for critically editing this manuscript.

This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This research was also supported in part by the Intramural Research Program of the National Institutes of Health, National Library of Medicine (Y.B.). Opinions expressed here are our own and do not reflect the view of the NIH, the Department of Health and Human Services, or the US government.

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Correspondence to Yīmíng Bào .

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Bào, Y., Kuhn, J.H. (2018). Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis. In: Salvato, M. (eds) Hemorrhagic Fever Viruses. Methods in Molecular Biology, vol 1604. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6981-4_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6981-4_3

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