Upload
anna-lamb
View
218
Download
0
Tags:
Embed Size (px)
Citation preview
Gramene Staff CSHL
Shuly Avraham (1/2) Payan Canaran (1/2) Ken Clark Chengzhi Liang Kiran Ratanapu Liya Ren Steve Schmidt Will Spooner (1/2) Lincoln Stein Wei Xhao (1/2)
Cornell Pankaj Jaiswal Molly Fogleman Susan McCouch Junjian Ni Immanuel Yap Greg Wilson
USDA Ed Buckler Terry Casstevens Doreen Ware
A Brief History 2000-2003
USDA CSREES/IFAFS + ARS 2003-2004
Bridge funding from NSF (continued ARS support)
2005-2007NSF + ARS
Specific Aims Under CSREES Migrate RiceGenes to a relational back
end. Curate major maps of rice, maize,
sorghum, wheat, barley & oats Generate comparative maps among
cereals Curate rice mutants, strains,
phenotypes & QTLs Assign GO terms to rice proteins
Specific Aims Under NSF All previous aims, plus… High density maize/rice comparative map Diversity module QTL & diversity modules Advanced query tool (BioMart) Genome annotation curriculum @
highschool level Open source genome annotation pipeline
Architecture
Internal Web Server External Web Server
Oracle
EnsEMBLSchema
MapSchema
OtherSchemas
Firewall
MySQL
NOEL UPDATE!Map Curation by SpeciesSpecies Map Sets
Rice 69
Maize 14
Sorghum 2
Barley 1
Oats 1
Wheat 1
Wild Rice 1
COMPLETE!Sequences Aligned to Rice
Proteins cDNAs + ESTs Genomic Marker Gene EnrichedRice Japonica 25,835 293,657 25,706Rice Indica 87,668Rice Brachyantha 34,930Rice Nivara 76,621Rice Rufipogan 53,049Maize 230,245 73,397 32,294 300,532Barley 286,652Sorghum 167,754 117 743 35,346Wheat 376,460 3,442Ryegrass 15,103 58,075Sugarcane 141,702Millet 694
Total Sequences 25,835 1,599,935 296,189 62,185 335,878Total Bases ??? ??? ??? ??? ???
UPDATE! Protein Curation Proteins from SwissProt/TREMBL Annotated with
Pfam, prosite, TMHMM, SignalP, Predotar
Associated to GO with Interpro2GO Associations manually reviewed 14,708 proteins assigned
13,319 proteins reviewed 16,722 of 35,065 associations reviewed