UserGuide:Genetic Map

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The Genetic Map is a very useful resource for forward genetic mapping. The WormBase Genetic Map inherited its look from ACeDB, however because of internet interface, many features have been changed.

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OVERVIEW OF DISPLAY

The Genetic Map can be accessed in two ways: either from the Genetic Map link of the Main Menu located at the top of every WormBase page, or from the Submenu located on each of the Gene Summary pages. When the Genetic Map is accessed via the Main Menu link, a whole-chromosome graphic display is first generated of chromosome I. To view a different chromosome, change the value in the pull down menu to the right of Chromosome Name and click the Change button.

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The viewable part of the chromosome with respect to the whole chromosome is indicated by the green bar that overlays a black vertical bar. On the left are loci commonly used for mapping that have been clearly ordered relative to one another. To the right, the black bars represent rearrangements and the grey bars identify and depict the extent of deficiencies and duplications in the region. The yellow bar represents the physical map (Contigs column), and next to it, genes that are ordered on the physical map. Inconsistencies between the physical and genetic maps are indicated by red marks next to the yellow bar. Loci that have been ordered on the genetic map are indicated on the right-most side of the window. Of these, cloned loci are highlighted in yellow.

MAP CONTROL

The graphical view of any individual chromosome can be changed in two ways: either by clicking the Shrink, Magnify, Up, or Down navigation links located under Map Control. Alternatively, it is possible to specify a chromosomal region of any size by entering numerical map coordinates. More detailed information about all of the loci, including deficiencies and duplications, can be retrieved by clicking on their names. For example, the end points of deficiencies and duplications and genetic map data can be accessed by clicking on any of the mapped loci.

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ACEDB MAP IMAGE SUBMENU

The map controls described above replace the menu links located inside of the map used originally for AceDB. These links are shown below. The other functions, Gmap data... and Highlight also do not function from this particular page.

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When the Genetic Map link is accessed from the submenu located on the top of each of the Gene Summary pages, a chromosome map is displayed centered upon the gene from which the map was accessed. For example, by clicking on the Genetic Map submenu link from the vab-10 page, vab-10 is highlighted in cyan and centered in the display. The viewable region cannot be altered from this page because there are no map controls. However, by clicking on the Gmap data, one can view a graphical representation of the results obtained from genetic mapping experiments. Rectangles indicate other markers used, and vertical lines indicate confidence information. Horizontal lines indicate where there are recombinants. The other AceDB menu buttons do not work in this window.

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OTHER WAYS TO ACCESS THE GENETIC MAP

From a Gene Summary page, there are at least 3 submenu options provided to access the Genetic Map: "Locus Summary", "Genetic Map" and "Acedb Image".

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When the Genetic Map is accessed from a Gene Summary Page, it is a graphic display of a gene, so the submenu is the same as Gene Summary Page.

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When the Genetic Map is accessed from the Main Menu, it is a graphic display of a chromosome, and the submenu is different from the Gene Summary Page:

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The default map display is "Acedb Image". Although the appearance is very similar to that people used to see in ACeDB, one very important thing is that users can no longer use the mouse to move or zoom the green bar on chromosomes. Instead, the "Map Control" now serves this purpose.