New Gramene Release!

[Claire Hebbard]

Dear Colleagues:

Gramene (http://www.gramene.org) is proud to announce the release #23 
of Gramene. For detailed information on the newest updates, please 
see the release notes at 
http://www.gramene.org/documentation/release_notes/releasenotes.html

Gramene web site features:
Species pages (http://www.gramene.org/species/) link to the species 
pages has been placed on the navigation bar at the top of page. These 
pages have been broken down into more but smaller pages, and the 
consistency of format between the species has been improved. Now you 
can navigate between species from any species page, not just from the 
introduction pages.

Gramene Data Summary for select species: The species pages now have a 
summary overview of all the genomic data for that specie in Gramene. 
For an example see the Rice Data 
http://www.gramene.org/oryza/rice_stat.html

Gramene DB statistics for the last year is now linked to the Gramene 
site map (http://www.gramene.org/sitemap.html). See the bottom left 
of this page and click on "DB Stats over Time" 
(http://www.gramene.org/dbstat/dbstat.html)

Gramene Database:

Genomes: Much new and updated data. Also, tree-based visualization of 
orthologs/paralogs for rice/maize/arabidopsis.

Maps: With this release, in addition to an update to CMap 0.16, all 
data (map sets, maps, features, and correspondences) in the Maps 
Module are built from the  Markers Module that have correlations, and 
the Gramene Annotated Nipponbare Sequence no longer includes all 
features on the Ensembl Rice Genome Assembly, but has only features 
that have correspondences to other maps. This was done to reduce 
visual clutter as well as improve server response time. All mappings 
are still present in the Markers Module and can be visualized in the 
Rice Genome Browser. The map set still includes all rice gene models. 
In addition, we have for the first added QTL to the map set. The Maps 
Module should be considered to be primarily a visualization tool and 
for comparative mapping. Users are encouraged to consult the Markers 
Module for primary information about markers, their mappings, and map 
set information.

Markers:  This release of Gramene marks the first time that the 
Markers Module contains all map sets, maps, and mappings. All 
visualizations in the Maps Module are now generated from the Markers 
Module.

Proteins:  The Gramene protein database provides curated information 
on SP-Trembl entries from family Poaceae (Grasses). The annotations 
include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and 
Predotar (plastid, mitochondrial and secretory pathway targeting) and 
Interpro assignments. Various ontologies such as Gene Ontology (GO), 
Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to 
provide functional characteristics.

Ontologies: We are making progress on integrating ontologies with 
other databases, as shown in their associations.

Genes: We're making progress in ontology associations to TO, PO or 
GO; new microRNA genes, and map position links.

QTL: New - when available you will find multiple links to QTL mapping 
positions and the inferred positions on the Gramene Annotated 
Nipponbare Sequence.

Pathways:  Version 1.2 of RiceCyc

Diversity:  The Diversity database has 626 germplasm accessions (587 
unique) and 524 SSR markers (247 unique) for rice; 48 germplasm 
accessions and 3802 SNP markers for wheat; and 302 germplasm 
accessions with SNP data, 1,543 germplasm accessions with SSR data, 
897 SNP and 520 SSR markers for maize.



-- 

Sincerely,
The Gramene Database Team


*****************************************************************
Gramene(www.gramene.org) is a curated, open-source, web-accessible 
data resource for comparative genome analysis in the grasses. Our 
goal is to facilitate the study of cross-species homology 
relationships using information derived from public projects involved 
in genomic and EST sequencing, protein structure and function 
analysis, genetic and physical mapping, interpretation of biochemical 
pathways, gene and QTL localization and descriptions of phenotypic 
characters and mutations.

*****************************************************************
This work is funded by the National Science Foundation (NSF) and the
USDA-Agricultural Research Service, and was previously funded by the USDA
Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful
to numerous collaborators and contributors for help in curation and for
sharing their datasets and tools.

*****************************************************************
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