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Phytozome: a comparative platform for green plant genomics
Open accessAbstract
The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.
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Gene Ontology: tool for the unification of biology
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., et al. (2009) · Nature · doi:10.1038/nature08064 · Cited by 1,065
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Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab688 · Cited by 1,925
One thousand plant transcriptomes and the phylogenomics of green plants
Initiative, O. T. P. T. (2019) · Nature · doi:10.1038/s41586-019-1693-2 · Cited by 1,734
SIFT missense predictions for genomes
Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M., & Ng, P. C. (2016) · Nature Protocols · doi:10.1038/nprot.2015.123 · Cited by 1,510
KBase: The United States Department of Energy Systems Biology Knowledgebase
(2018) · doi:10.1038/nbt.4163 · Cited by 1,624
Metadata
- Authors
- Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., & Rokhsar, D. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-22
- Volume
- 40
- Issue
- D1
- Pages
- D1178-D1186
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2141292707
- Cited by
- 5,420
- References
- 5
- FWCI
- 54.08
- Type
- journal article
- Language
- en
- Open access
- gold
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- Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., & Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr944
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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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