VectorNTI Graphics Display

To get started, double click on a sequence in one of the databases. The example shown below is using the TNF-alpha sequence downloaded in the previous section.

In this example, I have modified the size of the windows to increase the graphical view pane. You, too, can do this by clicking on the blue bars that divide each pane and dragging them around.

Mac Note: In several of the examples below we will right-click on a window. For Mac users, press the CTRL button and click the mouse. This will display the pop-up menu

The Active pane menu at the top of the page is context-sensitive. For example, clicking in the graphics pane will change that menu to buttons appropriate for graphics. Clicking in the sequence pane will change that menu to buttons appropriate for the sequence. Try this, by clicking through several windows.

The fields, or text, pane contains information about the sequence. You can expand this information by clicking on the + signs in the boxes like this:

This will allow you to view each of the different fields. For example, this sequence contains eight exons. (Click on the Feature Map folder to view).

The sequence window also contains a bar at the bottom that describes where you are. In this example I have selected 460 bp starting at position 111.

Sequence Pane Basics

There are several basic functions that you need to know how to perform. These are listed here. If you find anything missing from this list, please email with suggestions

1. Selecting Sequence
   To select sequence, click in the sequence window and hold the mouse button down while you move the mouse around. The amount and positions of the sequence that you have selected is shown in the bottom bar of the sequence window.
   You can then edit, copy, cut, or delete that sequence you have selected. Note that when the cursor moves to the 5' or 3' end of a sequence it changes to let you know where you are.
   
2. Locating where you are in a sequence
   If you pause with the mouse over some sequence the position of that sequence will be shown. This will quickly let you know where you are in a long sequence.
   
3. Translating sequence
   To quickly translate a sequence and view the translation in the sequence pane, select a region of the sequence. Right click (Mac users: control click) and select translate sequence. Note that you can translate forwards or backwards.
   
4. Copying formatted sequence
   See the camera section below.
   

Text (Fields) Pane Basics

There are several basic functions that you need to know how to perform. These are listed here. If you find anything missing from this list, please email with suggestions

1. Expand/Collapse Trees
   To expand a folder either double click on the folder or click on the little plus sign. To collapse a folder either double click on the folder or click on the little minus sign. Select a feature, right click, and choose collapse around will cause all other expanded features to close
   
2. Hyperlinks
   Many objects are hyperlinked. Clicking on an underlined object will download that from NCBI and open up a separate viewer. Depending on the source, the hyperlink may open in your WWW browser (e.g. Netscape or Internet Explorer)
   
3. Finding Features
   To find a feature on the sequence and graphical panes, right click on the feature, and then choose "Find Feature". The selection will be highlighted.

Changing the Graphical Display

The graphical display provides you with the most choices for altering the output. We will change several of the options on the graphical display by using the display setup

There are two ways that you can access the display setup:

1. Click the display setup button
2. Right click (Mac users: CTRL-click) on the graphics window, and select Display Setup

Both of these techniques will open the display setup box:

FMap Setup

This option allows you to add or remove features from the functional map. You can define CDS, introns, exons, etc that are displayed. However, many features appear to be present by default and there does not appear to be a mechanism to hide those features without deleting them from the Feature Map list in the text pane.

RMap Setup

This option allows you to define the restriction map display, choosing which enzymes are shown. Clicking the RMap Setup button will open the restriction map setup panel:



Here you can define which restriction enzymes to display by clicking on the add/remove buttons. You can also limit the restrictiion enzymes to blunt, 5', or 3' overhangs. From this panel you can also define the regions of sequence to include or exclude from the analysis.

To choose the restriction enzymes to add, first click remove all, and then click add. This will pull up a menu like this one:



You can sort any of the columns by clicking on the column header. For example, to sort by the restriction recognition site, click Recognition String. You can add more columns to this window by right clicking (or CTRL-clicking) on the header bar and selecting Columns... from the pull down menu (this should be the only choice!).

From the columns submenu you can add length, source, palindromes (or not), description, author, and many other fields. Note that if you add too many fields they will disappear off the right side of the box. You can alter this by putting the mouse over the line that divides the column headers and dragging the little bar sideways.

Motifs Setup

Choose which "motifs" are added to the display. Motifs are oligonucleotide sequences, and can either be exact matches or parital matches. You can load oligos from the oligo database, or you may enter a sequence de novo and use it in this.

ORFs Setup

Choose whether, and what size, open reading frames to display. This will bring up the ORF setup display box.



Here you can determine the minimum length of the ORFs to show. 50 or 100 nucleotides is usually a good starting point. You can decide the start and stop codons. (Defaults are start codons: ATG, GTG and stop codons: TAA, TGA, and TAG.)

The two check boxes, nested ORFs and stop codons, allow you to change how the ORFs are called. Nested ORF will also consider ORFs that have the same stop codon but different start codons, and the Include Stop Codon in ORF will use the stop codon as part of the ORF. The default is not to use it.

Sequence Setup

The sequence setup dialog allows you to alter the number of bases per line, and the number of blocks per line. It also allows you to choose between single- and double-stranded display, one- and three-letter amino acid codes, and select the font for the sequence.

Changing the look and feel

You can edit the graphics display by right clicking and choosing Graphics Display Setup or clicking the graphics display setup button. This will you to choose each of the elements in the display and set the color, size of the arrows/bars, hatchings, and so on.

Final Touches

Finally, you can manually edit each of the elements in the picture. Select Edit picture option from the right-click menu or click the edit picture button on the menu bar. You can now change any item in the picture simply by double clicking on it. You can change the original picture to something more manageable as shown below. Note that you can alter font faces, sizes, and colors. You can move elements around, and so on.

Exporting the Image

Once you have played with the image and got it looking just so, you probably want to export it into your favorite word processor or graphics program. To do so, choose Camera from the pull down menu, or click the camera button: . This will allow you to copy the whole screen either to clipboard or to a file. The clipboard is the most useful as you can paste it into whichever document you are working with.

With a little effort, the original image from TNF-alpha:

will end up looking like something much nicer:

In the next section, we will look at designing primers in vectorNTI.