Sequence View Markers

Step 1: Introduction

This tutorial was prepared using Genome Workbench version 3.5.0

It will take you through the steps of setting and manipulating new markers, showing marker information, changing marker properties, saving and deleting markers.

Step 2: Open molecule from GenBank

Launch the Genome Workbench. Click on File drop-down menu and select the Open menu item (or just click on the Open icon in the toolbar) to bring up the Open dialog. Select Data from GenBank on the left side of the dialog. Type in "NG_000007" in the entry box.

Click Next and then Finish to finish uploading. The system will display the new project in the project tree view.

Step 3: Open Graphical View on the imported molecule

Right click on the project item called "NG_000007" in the Project Tree View. Select Open New View… from the context menu.

Select ‘Graphical View’ in the next dialog. A Graphical View should be opened with at least Gene track available in a view (might see other tracks as well, depending on your track configuration) .

Step 4: Set new markers

Zoom the view into the [27,000-29,700] range. Place the mouse over the ruler bar on the top of the view. Right click to bring up the context menu. This context menu has a few options for marker creation.

Select Set New Marker At Position menu item. Change the marker name to "Marker1"and marker position to "28,000". Note that marker color is selected randomly. It can be changed now or later if desired.

Click OK to add a new marker.

Now select some region (for example [29,019-29,050]) and repeat the steps above using option Set New Marker for Selection to add the second marker named "Marker2” to the view.

Final view after adding two markers (Marker1 and Marker2):

Step 5: Show marker information

Place the mouse over the head portion of any marker. Right click to bring up context menu.

Click on Marker Details… menu item.

The marker information dialog (as shown below) will be displayed. For each marker it shows a list of locations across the marker position (note: for Marker2 detailed information is shown for the range start position) for the related sequences, such as NG sequences, mRNAs, and Proteins. It also shows the corresponding HGVS coordinates and the franking sequence around the marker position. Information about HGVS nomenclature can be found here: http://www.hgvs.org/mutnomen/.

The marker information dialog is a non-modal dialog. That means a user can manipulate the view while leaving the dialog open. The dialog will always stay on top of other views. For example, while the marker dialog is open, zooming or panning the graphical view is allowed. In addition, changing/adding/deleting markers inside the graphical view will automatically update the marker info shown in the dialog.

Step 6: Change marker properties

Change marker position by clicking and dragging

Place the mouse over the head portion of any marker. Press down left mouse button and drag the marker. After releasing the button, the marker information will be updated if marker info dialog is opened.

Change marker name/position/color through marker context menu

Rename Marker… menu item allows changing marker name. Modify Marker Name/Position/Color… menu item allows changing marker name, position, and color all at once.

Step 7: Delete markers

Markers may be removed from both the marker info dialog or marker context menu individually or all at once. Removing markers from one place (either view or info dialog) will update the other.

Step 8: Save markers

All added markers will be saved to the corresponding Genome Workbench project when the view is closed. Hence, if the same molecule is reopened from the same project, all the previously viewed markers will be added to the view. However, to save the marker permanently, one needs to save the corresponding Genome Workbench projects when exiting Genome Workbench.

Step 9: Conclusion

Congratulations, you have finished the markers tutorial! In this tutorial you have learned how to: Set new markers, View detailed marker information, Change marker properties, Delete markers, Save markers.