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<div><font face="Arial">Dear Colleagues:</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial">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</font
></div>
<div><br></div>
<div><b>Gramene web site features:</b></div>
<div>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.</div>
<div><br></div>
<div>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</div>
<div><br></div>
<div>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)</div>
<div><br></div>
<div><b>Gramene Database:</b></div>
<div><b><br></b></div>
<div><b>Genomes</b>: Much new and updated data. Also, tree-based
visualization of orthologs/paralogs for rice/maize/arabidopsis.</div>
<div><b><br></b></div>
<div><b>Maps</b>:<font color="#000000"> 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.</font></div>
<div><b><br></b></div>
<div><b>Markers</b>: <font color="#000000"> 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.</font></div>
<div><b><br></b></div>
<div><b>Proteins</b>: T<font color="#000000">he 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.</font></div>
<div><b><br></b></div>
<div><b>Ontologies</b>: We are making progress on integrating
ontologies with other databases, as shown in their associations.</div>
<div><b><br></b></div>
<div><b>Genes</b>: We're making progress in ontology associations to
TO, PO or GO; new microRNA genes, and map position links.</div>
<div><b><br></b></div>
<div><b>QTL</b>: New - when available you will find multiple links to
QTL mapping positions and the inferred positions on the Gramene
Annotated Nipponbare Sequence.</div>
<div><b><br></b></div>
<div><b>Pathways</b>: Version 1.2 of RiceCyc</div>
<div><b><br></b></div>
<div><b>Diversity</b>: <font face="Arial"> The Diversity database
has</font><font color="#000000"> 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.</font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial"><br></font></div>
<div><font face="Arial"><br></font></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div><font color="#000000"><br></font></div>
<div><font color="#000000">Sincerely,</font></div>
<div><font color="#000000">The Gramene Database Team</font></div>
<div><font size="-4" color="#000000"><br></font></div>
<div><font size="-4" color="#000000"><br></font></div>
<div><font size="-4"
color="#000000"
>*****************************************************************</font
></div>
<div><font color="#000000">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.</font></div>
<div><font color="#000000"><br>
*****************************************************************<br>
This work is funded by the National Science Foundation (NSF) and
the<br>
USDA-Agricultural Research Service, and was previously funded by the
USDA<br>
Initiative for Future Agriculture and Food Systems (IFAFS). We are
thankful<br>
to numerous collaborators and contributors for help in curation and
for<br>
sharing their datasets and tools.</font></div>
<div><font color="#000000"><br>
*****************************************************************</font
></div>
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<div><font color="#000000"><br></font></div>
<div><font color="#000000">To correspond with Gramene developers and
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<div><font color="#000000">of the e-mail (not the subject line) write:
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through the "Feedback" button at the top of the Gramene web
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