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Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences
Open accessAbstract
Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.
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Cites
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
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RESCRIPt: Reproducible sequence taxonomy reference database management
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Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community
Raja, H. A., Miller, A. N., Pearce, C. J., & Oberlies, N. H. (2017) · Journal of Natural Products · doi:10.1021/acs.jnatprod.6b01085 · Cited by 931
Canarini, A., Schmidt, H., Fuchslueger, L., Martin, V., Herbold, C. W., Zezula, D., Gündler, P., Hasibeder, R., Jecmenica, M., Bahn, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25675-4 · Cited by 384
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Edgar, R. C. (2018) · PeerJ · doi:10.7717/peerj.4652 · Cited by 319
Metadata
- Authors
- Deshpande, V., Wang, Q., Greenfield, P., Charleston, M., Porras-Alfaro, A., Kuske, C. R., Cole, J. R., Midgley, D. J., & Tran-Dinh, N.
- Venue
- Mycologia
- Publisher
- Informa UK Limited
- Published
- 2016-01
- Volume
- 108
- Issue
- 1
- Pages
- 1-5
- ISSN
- 0027-5514 (ISSN-L)
- 1557-2536
- OpenAlex
- W2260894375
- Cited by
- 204
- References
- 1
- FWCI
- 29.57
- Type
- journal article
- Language
- en
- Open access
- green
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- Deshpande, V., Wang, Q., Greenfield, P., Charleston, M., Porras-Alfaro, A., Kuske, C. R., Cole, J. R., Midgley, D. J., & Tran-Dinh, N. (2016). Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia. https://doi.org/10.3852/14-293
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