The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
Open accessAbstract
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
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BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Functional metagenomic profiling of nine biomes
Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., et al. (2008) · Nature · doi:10.1038/nature06810 · Cited by 980
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Kieft, K., Zhou, Z., & Anantharaman, K. (2020) · Microbiome · doi:10.1186/s40168-020-00867-0 · Cited by 1,123
Chen, I.-M. A., Chu, K., Palaniappan, K., Pillay, M., Ratner, A., Huang, J., Huntemann, M., Varghese, N., White, J. R., Seshadri, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky901 · Cited by 835
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)
Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., et al. (2019) · Nature Biotechnology · doi:10.1038/nbt.4306 · Cited by 732
Self-citationCultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4110 · Cited by 624
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Metadata
- Authors
- Paez-Espino, D., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V. M., Nielsen, T., Huntemann, M., K. Reddy, T. B., Pavlopoulos, G. A., Sullivan, M. B., Campbell, B. J., Chen, F., McMahon, K., Hallam, S. J., Denef, V., Cavicchioli, R., Caffrey, S. M., Streit, W. R., Webster, J., Handley, K. M., Salekdeh, G. H., Tsesmetzis, N., Setubal, J. C., Pope, P. B., Liu, W.-T., Rivers, A. R., Ivanova, N. N., & Kyrpides, N. C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10
- Volume
- 45
- Issue
- D1
- Pages
- D457-D465
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2543855063
- Cited by
- 187
- References
- 2
- FWCI
- 17.32
- Type
- journal article
- Language
- en
- Open access
- gold
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- Paez-Espino, D., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V. M., Nielsen, T., Huntemann, M., K. Reddy, T. B., Pavlopoulos, G. A., Sullivan, M. B., Campbell, B. J., Chen, F., McMahon, K., Hallam, S. J., Denef, V., . . . Kyrpides, N. C. (2016). IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Research. https://doi.org/10.1093/nar/gkw1030
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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