Viewing BayGenomics gene traps on Ensembl

How to view BayGenomics gene traps on Ensembl

Starting from the BayGenomics Web Site:

Note: Because Ensembl uses cookies, this process needs to be completed only once. Once completed, the BayGenomics track should appear on all subsequent visits to the Ensembl site.

To view BayGenomics gene traps on Ensembl, click on the Ensembl link located next to Genome Mapping on the cell line annotation page.

Clicking on Ensembl will bring up a new window that displays the Ensembl BLASTView of the gene tag. The cell line RRF211 was used for this example.

The red arrow indicates the best SSAHA hit.

In order to view the genome localization of the genetag, either click on the red [C] (for ContigView) listed under "Links" in the alignments section

or run the mouse over the red arrow, prompting a second, smaller window to pop up. Select Show in ContigView from this second window.

When the ContigView window appears, click on the DAS sources menu located in the "Detailed view" section. From this menu, select Manage Sources by clicking on it.

Clicking on Manage Sources will open a new window called Additional DAS sources. To add BayGenomics to the list of DAS sources, click the red Attach DAS button.

Type baygenomics.ucsf.edu/cgi-bin in the blank space listed in the "Other" category. Then, click on the red Show sources button.

Select BayGenomics by placing a check in the box next to it and click the red Attach DAS button. This will add BayGenomics to the list of DAS sources.

You will see a screen confirming that BayGenomics has been added. Click on the red Edit button to change some of the features of the BayGenomics track.

In order to see all the genetags that are available for the specific region in which you are interested, you must change the Max no of rows to display from 4 rows to Unlimited.

Click on the red Update button to confirm the changes. Then close the window by clicking on the red Close button in the upper right hand corner. Once the window is closed, refresh the Ensembl Contigview webpage. The BayGenomics gene traps located in that specific region of the genome will be displayed.

If you look at the list of DAS sources again, you will notice that BayGenomics has been added at the bottom of the list.