[Arabidopsis] Gramene's 34th database build released

Pankaj Jaiswal (OSU) via arab-gen%40net.bio.net (by jaiswalp from science.oregonstate.edu)
Wed Oct 19 11:35:43 EST 2011


The Gramene database team is happy to announce the 34th major release of 
the site.

Ref: http://news.gramene.org/?p=760

In our Ensembl genome browser, six genomes have been updated and we have 
added Glycine max (soybean), Selaginella moellendorffii, Chlamydomonas 
reinhardtii bringing us to 22 genomes.

We have also updated the genome browser to Ensembl version 62, updated 
blastz-chain-net whole genome alignments for new and updated genomes, 
built new Compara (homology) gene trees, and updated protein domain 
annotations, cross-references and gene ontology (GO) projections.

The BioMart data mining tool has updated plant gene and variation 
databases.

Our ontologies database has been updated to the latest releases of GO, 
plant ontology (PO), and trait ontology (TO) and includes many new 
associations to the genomes and genes of our new species.

Our Pathways section now has official release versions of MaizeCyc and 
BrachyCyc, and non-plant pathways were removed from RiceCyc,SorghumCyc, 
and BrachyCyc.

The diversity section contains a new rice study of 14 agronomic traits 
from 226K SNPs across 374 lines from Huang X, et al, Nat Genet 2010, the 
3.06 version of NSF Arabidopsis 2010 Project 250K chip study, phenotype 
data from single-gene studies, and a new association viewer for 
Arabidopsis variation data which is also linked from our Arabidopsis 
Ensembl genome browser.

Several Oryza germplasm have been added to our germplasm database to 
bring the total to 13,265 records with links to Gramene’s markers, map 
sets, genes and proteins.

Our distributed annotation server (DAS) has been updated with the latest 
alignments for all our species.  Please let us know if you have and 
problems or question with the new build.

http://news.gramene.org/?p=760

--
Ken Youens-Clark
kclark from cshl.edu
Ware Lab/CSHL/USDA-ARS




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