A Database for Triticeae and Avena
In CMap, a map is a linear array of interconnected
features. This could represent a single linkage group in the
case of a genetic map, or a single contig for physical maps.
Related maps are grouped into map sets. Generally, these
are the result of a particular study, such as the set of linkage
groups produced by a genetic mapping study. For more
information about the map sets contained in the database, visit
the Map Set Info page.
To set up a comparison, a user first selects a reference map
set, then a reference map. This serves as the basis for
any comparisons that the user chooses to make. Once the
reference map image has been rendered, the user is given the
option to select one or two comparative maps. These
comparative maps may be added to both the left and the right of
the reference map. The user may keep adding additional maps for
as long as valid comparisons are available.
Any item that is positioned on a map is called a feature.
The position may be either a point or an interval. Different
feature types are represented by different shapes (such
as horizontal tick marks [for points], line intervals, boxes,
arrows, etc.) or different colors. For more information on any
feature, click on it to view the corresponding feature
The lines that connect features on one map to features on
another map denote correspondences. These
correspondences are assigned either automatically (based on
feature name) or manually by the data curator to designate
features on different maps that are equivalent in some manner.
Different colors represent different correspondence
Once a user has selected a reference map set and a reference
map, it is immediately rendered as a map image. By default, the
entire length of the map is displayed. At the top of the image
is a box in which is printed the species, map set name, and map
name as well as a combination of the following controls:
A vertical scale bar indicates positions along the length of the
map. The distance measure (e.g., cM) being used is printed at
the bottom of the scale bar. Features are drawn at appropriate
positions. A legend for the various feature types shown on the
map is printed at the bottom of the image. Click on a feature
label to view the feature
details page for that feature.
Note that not every feature may be labeled. The drawing
algorithm will try to fit as many labels as it can, until there
is no more available space. To see more labels, you may wish to
increase the image size or decrease the font size. You may also
specify "Start" and "End" positions to zoom in to a particular
region on the reference map.
If two or more maps are being compared, each map will be drawn
in a separate regions. Adjacent maps will have correspondence
lines that connect corresponding features. The color of the
line depends on the type of correspondence, indicated in the
legend at the bottom of the map image.
In the lower-right-hand corner is a watermark indicating the version
of CMap used to draw the map. This is also hyperlinked to the CMap
CMap is free software from the GMOD
GrainGenes is a product of the US Department of Agriculture.