Rat Stand-alone GViewer (Genome Viewer) Help

The Genome Viewer (GViewer) tool provides diagrams displaying genome wide chromosome locations of genes and QTLs annotated to the query results.  Users have the options to view all the objects, to export data as a CSV file or to overlay more objects in the resulting diagram.  The GViewer appears in a number of places on the RGD website, for instance a GViewer image appears on the ontology report pages.  Also, you can view the results of a general search in GViewer by clicking the link on the search results page.  GViewer is also available as a stand alone tool.  The advantage of this tool is that it allows you to search for multiple terms across multiple ontologies using "Boolean" queries, i.e. you can search for objects annotated to both Term1 AND Term2, either Term1 OR Term2, Term1 but NOT Term2, and so on.

This page gives information about using the stand-alone GViewer.  Click here for information about the GViewer as part of the ontology report page, or click here for information about the general search and how to access GViewer from the search results page.

The search tool in GViewer allows users to search by partial or exact ontology terms. Users can filter results by checking boxes under ontology types.

Once the search is completed,  a GViewer diagram is generated displaying the genomic positions of  all rat genes and QTLs annotated with the term results. These genetic objects –genes in dark red , qtls in blue- are shown to the right of each chromosome.  Clicking on a chromosome opens a zoom pane which gives a closer look at objects mapped to the selected area. A second click locks the slider in a fixed location.  Links to the object report page are accessible by clicking on object symbols in the zoom pane.

To the upper right of the zoom pane, there are two links allowing users to zoom in to have a closer look of the chromosome region or to zoom out to get a view of a bigger region. The “Send to GBrowse” link will send the position information of the selected chromosome region  to the RGD Genome Browser (GBrowse). A full set of genes and QTLs in the region of interest is displayed in GBrowse to give a more complete view of genomic data in that area.

List All Objects

Clicking on this link at the bottom left on the diagram will display a list of all the objects in the diagram grouped by chromosome. Clicking on an object symbol will put the object and flanking chromosome regions into the zoom pane.


CSV export

Clicking this link allows exporting the data as a CSV file. Users have the option of downloading all objects, objects shared by multiple searches or unique objects.


Add objects

This function allows overlaying additional objects to the current GViewer diagram. Clicking this link will bring up the window “Add objects to the Viewer.”  Users have options to search for genes, QTLs, markers or ontology terms and to display them in customized colors different from the existing objects in the current diagram. Clicking on one of the options will bring up the “Enter Keyword”  window.  Users can enter a search term for gene symbol, QTL symbol, marker symbol or an ontology term. The example here is a QTL search with keyword "bp215" and brown color is picked for display. The search returns one QTL, Bp215.


Clicking on the symbol, Bp215, will  show the object's  location along with other existing objects in the zoom pane.  The  yellow  color indicates that this object was already displayed by the previous search. Click here for more help on GViewer.