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Gramene 2013: comparative plant genomics resources Public Deposited

https://ir.library.oregonstate.edu/concern/articles/k06989337

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  • Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.
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  • Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., ... & Ware, D. (2014). Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42(D1), D1193-D1199. doi:10.1093/nar/gkt1110
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  • National Science Foundation [IOS-0703908 and IOS-1127112]; United States Department of Agriculture—Agricultural Research Service [413089, 418046 and 418047 to D.W.]; European Community’s 7th Framework Programme (FP7/2007-2013; Infrastructures) [contract # 283496 to P.K.]; United Kingdom Biotechnology and Biosciences Research Council [BB/J000328X/1, I008071/1 and H531519/1 to P.K.]; The infrastructure and intellectual support for the development and running the Plant Reactome is supported by the Reactome database project via a grant from the US National Institutes of Health [P41 HG003751 to L.S.], EU grant [LSHG-CT-2005-518254] ‘ENFIN’, Ontario Research Fund and the EBI Industry Programme. Funding for open access charge: Gramene Project NSF grant [IOS-1127112].
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  • description.provenance : Made available in DSpace on 2014-04-21T16:33:16Z (GMT). No. of bitstreams: 2 DharmawardhanaPalithaBotanyPlantPathologyGramene2013.pdf: 7224382 bytes, checksum: 7e70d8966a8076319e3a5502d5aa9a0d (MD5) DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf: 198839 bytes, checksum: 8253e3e064922530abb9e4b576b76dd0 (MD5) Previous issue date: 2014-01-01
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  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-04-21T16:33:16Z (GMT) No. of bitstreams: 2 DharmawardhanaPalithaBotanyPlantPathologyGramene2013.pdf: 7224382 bytes, checksum: 7e70d8966a8076319e3a5502d5aa9a0d (MD5) DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf: 198839 bytes, checksum: 8253e3e064922530abb9e4b576b76dd0 (MD5)

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