Gramene Tips Archive

Enter the Matrix to discover the best maps to compare to each other.

You can search different protein or nucleotide databases with Gramene's BLAST tool.

You can view/download Gramene's files. Use the Download and FTP pages.

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

Even experienced users may learn something new if they view the Gramene Tutorials.

Gramene has maps for 27 grass species.

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

You can download and install Gramene and the comparative map viewer, CMap.

Find proteins, genes, maps, and QTL for your favorite species by using the Taxonomy Ontology.

You can contact Gramene either by e-mailing the public list-serve at gramene@gramene.org 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.

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.

Gramene has raw phenotype and genetic data from rice QTL population studies, searchable by population name. Eg. Jefferson x rufipogon population.

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

Species pages 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.

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.

Users can submit gene information to Gramene.

Users can submit ontology (controlled vocabulary) information to Gramene.

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.

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

The Marker database 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.

You can limit your BLAST search in Gramene to a specific plant species.

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

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

Search species using synonyms. For example, Pennisetum, Pennisetum glaucum, Pennisetum americum, and Pearl millet are synonyms, but produce different search results. See Ontologies to find synonyms.

To find out the meaning of a term or abbreviation, check the Gramene Glossary.

Gramene hosts an electronic version of the Rice Genetics Newsletter.

Gramene provides information on primers and PCR conditions in the Markers Module.

Gramene has sequence, genetic, QTL, physical and deletion maps.

For emails on database releases and the Gramene Newsletter, join Gramene's announcement mailing list or view the mailing list archive.

Gramene's source of gene predictions is the TIGR rice database.

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 maize FPC maps as comparative maps.

  

Last modified: Thu Nov 4 11:56:57 2004