The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Open accessAbstract
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
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Gregory, A. C., Zayed, A. A., Conceição-Neto, N., Temperton, B., Bolduc, B., Alberti, A., Ardyna, M., Arkhipova, K., Carmichael, M., Cruaud, C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.040 · Cited by 826
Self-citationBacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Shkoporov, A. N., & Hill, C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.017 · Cited by 767
Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Self-citationThe Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Gregory, A. C., Zablocki, O., Zayed, A. A., Howell, A., Bolduc, B., & Sullivan, M. B. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.003 · Cited by 658
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Metadata
- Authors
- Bolduc, B., Jang, H. B., Doulcier, G., You, Z.-Q., Roux, S., & Sullivan, M. B.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2017-05-03
- Volume
- 5
- Pages
- e3243
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W2610784236
- Cited by
- 287
- References
- 58
- FWCI
- 15.23
- Type
- journal article
- Language
- en
- Open access
- gold
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