Panzea Graphical Map Viewer

From this utility you can define your own graphical map displays of all of the maize or teosinte genes and markers used in our project with known or estimated map positions. This page provides a highly simplified version of the full CMap viewer interface.

To begin, choose your desired View type (genetic or physical). Under the genetic view, two genetic map sets are available for display (Select one). The first shows the positions of our Panzea genes, loci and markers on the IBM2 2005 Neighbors map of maize. The second consists of 290 SNPs, SSRs, indels and CAPs mapped in a teosinte/maize backcross population. Under the physical view, a single physical map is available, showing the positions of Panzea loci on the contigs of the AGI Maize Agarose FPC physical map.

Next, choose which Chromosome to view. If you initially requested a genetic map view, the fields for Region of genetic map will then automatically fill in with the smallest and largest cM positions on the chosen chromosome. Modify these to display a smaller region if you wish. If you initially requested a physical map view, the scroll box for Contig on physical map will then automatically list all contigs that anchor to the selected chromosome. Use the scroll bar to help you view all of these contigs, and select one or more to view. You can select multiple, contiguous contigs for display if you wish, using the shift key and your mouse, or multiple, non-contiguous contigs with the control key and your mouse. Contigs are numbered in order relative to their chromosomal position.

Finally, choose the Features to display on your graphical map, then click on the Display map button underneath the feature list to see your customized graphical map. From there, you can then use the powerful features of the full CMap viewer interface to further customize your graphical map view. Also, for some predifined map views and some background info on the maize genetic and physical maps, click here.

Download a Graphical Map Viewer tutorial.