User Frequently Asked Questions

Answers to User Frequently Asked Questions

How do I activate or edit my license?

In the menu bar, go to the File -> license -> edit license tab. This opens a dialogue where you can enter or edit your license information. You need to be on the internet to activate the license. After activation, you can use Vectors offline. However, one session in five needs to be online at start-up for a license check to happen.

What is the home folder and how does it work?

The home folder makes it easier to open GenBank format .gb files in Vectors. The names of .gb files in your home folder show up in the Navigator window and you can simply double-click on the file name to open the file. Your home folder is set up on your first use of Vectors. To change your home folder go to File -> Change Vectors folder in the menu bar. To open .gb files that are not located in your home folder, use the File -> Open option in the menu bar.

How do I open my sequence and vector files in Vectors?

Currently, Vectors works with files in the Genbank .gb format. The easiest way to open these files is by moving them into your Vectors home folder. The file names will then by available in the Navigator window in Vectors and you can open them by double-clicking on them. For sequence files that are not in the .gb format, there are freely available online file format conversion tools available here and here. Alternatively, you can open a new file in Vectors and then cut and paste in the sequence information.

How do I adjust the workspace in Vectors?

All of the different viewing areas in Vectors (i.e. Navigator, Features Window, Vector Window, Sequence Window, Canvas) can be resized to suit your work needs by putting the cursor on the window boundaries (in Windows) or the little dots between windows (in Macs) and then clicking and pulling on them. Once the window size is reduced beyond a minimal size, it will close itself. The window can be reopened by moving the cursor to the edge where the window should be and clicking and pulling to open the window.

The Vector window that shows the vector map can be split vertically into two windows to work with two different vectors side-by-side, by opening a second vector and then drag-and-dropping the tab for the second vector into the Vector window. Similarly, drag-n-dropping the vector tab of a second Vector window into the first Vector window reverts to a single Vector window.

What is the 'Canvas' and how does it work?

The 'Canvas' is like a painting canvas for DNA vectors, where you can easily assemble ('paint') new vectors by drag-n-drop cloning. This functionality is the heart of Vectors. You can select DNA fragments to drag-n-drop into the Canvas in several ways:

  1. Restriction selection. To select a DNA fragment generated by restriction digestion, first make sure the desired restriction sites appear in the main Vector window by selecting restriction enzymes in the Analysis -> Restriction menu item and the Restriction window. Once the restriction sites are present in the Vector window, sequentially click on the desired two restriction site labels in the Vector window. The desired DNA fragment will now be selected and can be drag-n-dropped into the Canvas. This fragment will have ends that reflect the restriction enzymes used to generate the fragment.
  2. Mouse selection - Sequence window. Select the desired DNA fragment with the mouse in the Sequence window. The corresponding region will be shown as selected in the Vector window and can be drag-n-dropped from the Vector window to the Canvas.
  3. Input selection. Click the select button in the Sequence Window and manually enter the start and end positions of the desired DNA fragment. The fragment will be selected in the Vector Window for drag-n-dropping.
  4. Feature selection. Click on a feature in the Vector window, such as a gene, to select it for drag-n-dropping to the Canvas.
  5. PCR selection. Click on the PCR button in the Sequence window. In the dialogue that opens, enter the primer sequences that define the PCR fragment you wish to manipulate. 'Extension' refers to 5' extensions to the primer for the introduction of new sequence to the target fragment. The corresponding PCR product is generated as a new fragment in a new Vector window. This enables the fragment to be further restriction digested, if desired, before drag-n-dropping the PCR product into the Canvas.

Is there a way to do cloning using PCR primers in Vectors?

Yes. Click on the PCR button in the Sequence window. In the dialogue that opens, enter the primer sequences that define the PCR fragment you wish to manipulate. 'Extension' refers to 5' extensions to the primer for the introduction of new sequence to the target fragment. The corresponding PCR product is generated as a new fragment in a new Vector window. This enables the fragment to be further restriction digested, if desired, before drag-n-dropping the PCR product into the Canvas.

How do I work with multiple vectors simultaneously?

Each time a new vector is opened, a new tab for the vector is created in the Vector window. By clicking on the tab, the corresponding vector will be seen in the Vector window and the sequence window. To see side-by-side graphical representations of two vectors, a vector tab can be clicked on and drag-n-dropped into the Vector window. This action will create a new Vector window by splitting the original Vector window vertically. By pulling the tab of a second Vector window into the first Vector window, the vector moves into the first Vector window. If this was the only vector in the second Vector window, the second Vector window closes. Multiple Canvas windows can be opened simultaneously with similar detachable tabbing behaviour.

How do I edit vector features?

Double-click on the feature attribute (i.e. name, start/end position) in the Features window to enter edit mode, and then enter the new information. Right-click in the Features window to add/remove features.

How do I make new vectors?

Click on the 'New' button in the Menu bar. New vectors are created with a minimum of information (i.e. the vector name and whether it is linear or circular). To edit the sequence of a new vector, go to the Sequence window and click on the 'Edit' button. Then paste or enter new sequence, replacing the initial placeholder 'AA' bases.