TY - JOUR
AU - Marcela Monaco
AU - Joshua Stein
AU - Sushma Naithani
AU - Sharon Wei
AU - Palitha Dharmawardhana
AU - Sunita Kumari
AU - Vindhya Amarasinghe
AU - Ken Youens-Clark
AU - James Thomason
AU - Justin Preece
AU - Shiran Pasternak
AU - Andrew Olson
AU - Yinping Jiao
AU - Zhenyuan Lu
AU - Dan Bolser
AU - Arnaud Kerhornou
AU - Dan Staines
AU - Brandon Walts
AU - Guanming Wu
AU - Peter D'Eustachio
AU - Robin Haw
AU - David Croft
AU - Paul Kersey
AU - Lincoln Stein
AU - Pankaj Jaiswal
AU - Doreen Ware
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.
BT - Nucleic acids research
C1 - http://www.ncbi.nlm.nih.gov/pubmed/24217918?dopt=Abstract
DA - 2014 Jan
DO - 10.1093/nar/gkt1110
IS - Database issue
J2 - Nucleic Acids Res.
LA - eng
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.
PY - 2014
SP - D1193
EP - 9
T2 - Nucleic acids research
TI - Gramene 2013: comparative plant genomics resources.
VL - 42
SN - 1362-4962
ER -