CMap refers to the Comparative Map Viewer, a tool that is used to compare two or more maps, whether they are different types of maps, maps of different species, or a combination. The module's new title of "Maps" more accurately reflects the contents of the module, which includes many different types of maps and maps from different species, as well as the CMap tool used to compare them.

Yes. Please refer to the Maps help documents, tutorial and release notes at http://www.gramene.org/tutorials/cmap.html. The Maps Help files are also very useful.

In Maps, you can determine the location of a particular trait or marker and to which grass species they have been mapped. The comparative map viewer tool (CMap) allows a user to draw comparisons between different maps. These maps can be of different type (e.g., genetic and physical) and from different species (e.g., rice and maize). Users can view where genes, markers, and QTL are located in one grass species compared to where they may be located in a number of other grasses. You can examine the colinearity of a particular region in one species with another, or infer which linkage group in one species is most conserved with a linkage group in another species. Users can also determine which maps are the best to compare to each other using the maps Matrix (http://www.gramene.org/db/cmap/matrix), which shows the number of correspondences between maps.

Maps and CMap run on a relational database. Oracle, MySQL, Sybase and PostgreSQL are currently supported

CMap is a part of GMOD. You can download the latest release from SourceForge (http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129). Visit the GMOD / CMap home page (http://gmod.sourceforge.net/cmap/index.shtml) for more information.

Gramene maps come from a number of sources including published data, other genome databases and direct contributions. In addition, Gramene generates its own rice sequence map. This is based on the TIGR assembly for the rice genome and integrates markers, ESTs, proteins and other information from rice and other crops.

In Maps, a map is a single chromosome, linkage group, or contig. A map set is the set of maps produced by a single mapping study. This usually covers all the chromosomes or linkage groups in the genome.

Gramene currently has genetic, QTL, physical, sequence, and deletion maps. Visit the Map Type Info page (http://www.gramene.org/db/cmap/map_type_info)for more information on each type.

Click on "Map Sets" in the Maps submenu to view the Map Set Info page (http://www.gramene.org/db/cmap/map_set_info), which lists all the map sets in Gramene.

In Release 19 (Dec 2005) Gramene had maps for 22 species of rice, wild rice, barley, oat, rye, wheat, maize, sorghum and millet. Check the Maps Species Info page (http://www.gramene.org/db/cmap/species_info) for the latest information.

In the Map Set Info page (http://www.gramene.org/db/cmap/map_set_info), select a species from the "Restrict by Species" drop-down list, then click on the "Submit" button.

[OBSOLETE] is placed next to a map set name when the map set has been supplanted by a later version.

The Matrix (http://www.gramene.org/db/cmap/matrix) is a cross-tabulated table showing the number of correspondences between all pairs of map sets. You can use it to search for map comparisons that have a higher number of correspondences, giving the user an indication that they will be more informative.

Markers are the procedures and reagents, such as RFLP probes and SSR primers, used to map features. A feature is a specific position on a specific map in a specific map set. Hence, a single marker may have been used to map multiple features in different map studies. Marker information is stored in a separate Gramene module (http://www.gramene.org/markers/index.html).

When we curated the genetic positions for those genes, we found several genes whose positions were detected in historical studies, and those studies generally only involved a very small number of markers and the linkage information was frequently limited to two- or three-point analysis. It is very difficult for us to curate and display all those original maps and markers related to the genes. In order to solve that issue, we created the "interpolated phenotype" concept to curate those genes. Briefly we try to identify closely linked markers to a particular gene from the original mapping study, and we check whether those linked markers have been mapped on several commonly used genetic maps. Based on the info we get, we determine the map positions of the gene on the commonly used genetic maps and anchor genes to those maps.

As of July 2006: Cornell BS125/2/BS125/WLO2 RFLP 2001; Cornell IR64/Azucena SSR 2001; JRGP Nipponbare/Kasalath RFLP 2000; Cornell BS25/2/BS25/WLO2 RFLP 1994; IRMI Integrated SSR 2003; Hokkaido Morphological 2000; IGCN ZhaiYeQing 8/JingXi 17 1998;