TY - JOUR
T1 - Gramene 2013
T2 - Comparative plant genomics resources
AU - Monaco, Marcela K.
AU - Stein, Joshua
AU - Naithani, Sushma
AU - Wei, Sharon
AU - Dharmawardhana, Palitha
AU - Kumari, Sunita
AU - Amarasinghe, Vindhya
AU - Youens-Clark, Ken
AU - Thomason, James
AU - Preece, Justin
AU - Pasternak, Shiran
AU - Olson, Andrew
AU - Jiao, Yinping
AU - Lu, Zhenyuan
AU - Bolser, Dan
AU - Kerhornou, Arnaud
AU - Staines, Dan
AU - Walts, Brandon
AU - Wu, Guanming
AU - D'Eustachio, Peter
AU - Haw, Robin
AU - Croft, David
AU - Kersey, Paul J.
AU - Stein, Lincoln
AU - Jaiswal, Pankaj
AU - Ware, Doreen
N1 - Funding Information:
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. The funders had no role in the study design, data analysis or preparation of the manuscript. Funding for open access charge: Gramene Project NSF grant [IOS-1127112].
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkt1110
DO - 10.1093/nar/gkt1110
M3 - Article
C2 - 24217918
AN - SCOPUS:84891793130
SN - 0305-1048
VL - 42
SP - D1193-D1199
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -