The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences
Open accessAbstract
DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee .
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QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Cited by
Fungal diversity notes 603–708: taxonomic and phylogenetic notes on genera and species
Hyde, K. D., Norphanphoun, C., Abreu, V. P., Bazzicalupo, A., Thilini Chethana, K. W., Clericuzio, M., Dayarathne, M. C., Dissanayake, A. J., Ekanayaka, A. H., He, M.-Q., et al. (2017) · Fungal Diversity · doi:10.1007/s13225-017-0391-3 · Cited by 307
Nagy, L. G., Kocsubé, S., Csanádi, Z., Kovács, G. M., Petkovits, T., Vágvölgyi, C., & Papp, T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049794 · Cited by 117
Metadata
- Authors
- Abarenkov, K., Tedersoo, L., Nilsson, R. H., Vellak, K., Saar, I., Veldre, V., Parmasto, E., Prous, M., Aan, A., Ots, M., Kurina, O., Ostonen, I., Jõgeva, J., Halapuu, S., Põldmaa, K., Toots, M., Truu, J., Larsson, K.-H., & Kõljalg, U.
- Venue
- Evolutionary Bioinformatics
- Publisher
- SAGE Publications
- Published
- 2010-01
- Volume
- 6
- ISSN
- 1176-9343 (ISSN-L)
- OpenAlex
- W1978431551
- Cited by
- 301
- References
- 4
- FWCI
- 15.64
- Type
- journal article
- Language
- en
- Open access
- gold
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- Abarenkov, K., Tedersoo, L., Nilsson, R. H., Vellak, K., Saar, I., Veldre, V., Parmasto, E., Prous, M., Aan, A., Ots, M., Kurina, O., Ostonen, I., Jõgeva, J., Halapuu, S., Põldmaa, K., Toots, M., Truu, J., Larsson, K.-H., & Kõljalg, U. (2010). PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences. Evolutionary Bioinformatics. https://doi.org/10.4137/ebo.s6271
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
