
Even experienced users may learn something new if they view the <A 
HREF="/tutorials/">Gramene Tutorials</A>.
%

Gramene has maps for 
<a href="/db/cmap/species_info">26 grass species</a>.
%

The <a href="/markers/index.html">Marker database</a> contains all map 
sets, maps, and mappings, and should be considered to be the primary 
source for information about maps and markers of various types.
%

The Gramene protein database provides information on SP-Trembl
entries from rice and other grass species such as Aegilops, Avena, Hordeum,
Lolium, Pennisetum, Saccharum, Secale, Sorghum, Triticum, and Zea.
%

The SSR Marker Resource is listed under the Marker database, and offers SSRIT, a list of common markers, and primer information from McCouch lab.
%

Gramene hosts an electronic version of the <a
href="/newsletters/rice_genetics/">Rice Genetics
Newsletter</a>.
%

All visualizations in the CMap views (mapsets, maps, features, and 
correspondences) are generated from the Markers Module.
%

To find out the meaning of a term or abbreviation, check the
<a
href="/documentation/glossary/index.html">Gramene
Glossary</a>.
%

<A HREF="species/index.html">Species pages </A>offer detailed information on different 
cereal species and links to their data in Gramene. These pages can 
be accessed via the images on the species bar at the bottom of each page. 
%

You can contact Gramene either by e-mailing us at <a
href="mailto:gramene@gramene.org">gramene@gramene.org</a> or by
sending a question to the curators and developers at Gramene on any
page by selecting the Feedback button in the top right hand corner.
%

For updates on releases and other information, join <a
href="/mailarch/index.html">Gramene's mailing
list</a> or view the mailing list archive. 
%

The use of ontologies provides a strong framework for integrating the 
data between the Gramene modules.
%

Enter the <a href="/db/cmap/matrix">Matrix</a> to
discover the best maps to compare to each other.
%

You can <a
href="/documentation/gramene_installation.html">
download and install</a> Gramene and the comparative map
viewer, CMap.  
%

You can view/download Gramene's files.  Use the <a
href="/download/">Download</a> and <a
href="ftp://ftp.gramene.org/pub/gramene/">FTP</a> pages.
%

Users can <a
href="/rice_mutant/gene_submit.html">submit</a>
gene information to Gramene. 
%

Users can submit <a
href="/plant_ontology/submission">ontology
(controlled vocabulary)</a> information to Gramene.  
%

You can search different protein or nucleotide databases with
<a href="/Multi/blastview">Gramene's BLAST
tool</a>.
%

You can limit your <a
href="/Multi/blastview">BLAST</a> search in
Gramene to a specific plant species.
%

The rice genome assembly is still being finalized and therefore
marker and clone positions along pseudomolecules may change with a
Gramene build.  Each successive build brings improvements.  Previous
Gramene builds are archived.
%

Gramene's source of gene predictions is the <a
href="/db/literature/pub_search?ref_id=8051">TIGR</a>
rice database. 
%

Gramene has 
<a href="/db/cmap/map_type_info">sequence,
genetic, QTL, physical and deletion maps</a>.
%

Map details can be downloaded in a tab-delimited format so that users can work with the data in a spreadsheet program. 
%

Gramene provides information on <a
href="/markers/index.html">
primers and PCR conditions</a>.
%

The QTL Power Search can help to make your searches more exact.
For example, if searching for linkage group 1* in the QTL simple
search, results would include linkage groups 11 and 12 as well.  With
the Power Search, users are able to exclude 11 and/or 12.  
%

The AGI Maize FPC maps cannot be viewed directly, because they are not
reference maps.  If you are looking for them, start with a maize
genetic map or the rice sequence map as a reference map, then add the <a
href="/db/cmap/viewer?refMenu=&compMenu=1&optionMenu=&addOpMenu=&ref_map_start=&ref_map_stop=&min_correspondences=&comp_map_set_left=&comp_map_set_right=agimf1104a&comparative_map_right=-1&sub=Redraw+Map&highlight=&ft_DEFAULT=&ft_marker=2&evidence_type_ANB=1&ets_ANB=0&evidence_type_INS=1&ets_INS=0&evidence_type_NB=1&ets_NB=0&aggregate=1&cluster_corr=2&magnify_all=1&image_size=medium&font_size=large&image_type=png&label_features=all&collapse_features=1&scale_maps=1&stack_maps=0&clean_view=0&show_intraslot_corr=0&split_agg_ev=0&comp_menu_order=display_order&ref_map_set_aid=ibm2n04&ref_map_aids=ibm2n04-1&modified_ref_map=&ref_species_aid=maize&comparative_maps=&modified_comp_map=&flip=&data_source=Gramene">maize
FPC maps</a> as comparative maps.
%

Find proteins, genes, maps, and QTL for your favorite species by using 
the <a href="/db/ontology/search_term?id=GR_tax:013969">Taxonomy Ontology</a>.
%

Search using synonyms. For example, Pennisetum, Pennisetum glaucum, Pennisetum americum, and Pearl millet are synonyms, but produce different search results. See <A HREF="/plant_ontology/">Ontologies</A> to find synonyms.
%

Refer to module home pages, tutorials, help files and release notes for tips on conducting searches.
%

Researchers who have published data that is not currently in the Gramene 
database are encouraged to contact Gramene to request curation of their 
article.
%

Gramene has raw phenotype and genetic data from rice QTL population studies, searchable by population name. Eg. <A href="http://http://dev.gramene.org/db/diversity/diversity_view?action=view&object=div_experiment&id=7">Jefferson x rufipogon population</A>. 
%