Source: http://www.basic.northwestern.edu/VectorNTI/Documentation/VectorNTI/chapter1.htm

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Chapter 1. Display Windows

Background

This chapter introduces you to the Vector NTI interface and Display windows, which are Vector NTI’s primary means for displaying and manipulating DNA/RNA/ protein molecules and gels.

Your Task: Creating Display windows and work with graphics, sequence, and text

Your task will be to create Molecule Display windows for the molecule pBR322, and inspect the information the Display windows contain. In this chapter you will also learn to manipulate graphics, sequences, and text. In this chapter we will show you how to use the information in the text pane and how to display amino acid translations of the nucleotide sequence. We will also show you how to open amino acid molecules.

In Chapter 2 of the tutorial, we will demonstrate how to edit a molecule sequence and feature map in a Molecule Display window.

In Chapter 3 we will show you how to move and format objects in the graphics pane.

Follow the steps in the order shown. Figures show what your screen should look like at various points along the way.

1. Launch Vector NTI

Launch Vector NTI by double-clicking its icon in the program group or folder in which you installed Vector NTI.

When you start Vector NTI for the first time after installation, Vector NTI creates an empty database and asks permission to import an initial set of database objects from Vector NTI archives installed in the Vector NTI working folder or directory. Press the OK button in the confirmation dialog box. The DNA molecules, proteins, enzymes, oligos, and gel markers will be imported to form the initial Vector NTI database.

2. Inspect the Vector NTI workspace and Database Explorer windows

Vector NTI first appears on the screen with an empty workspace:

Next to the workspace window, the Database Explorer window is opened, showing the contents of a DNA/RNA molecules or Proteins table (depending on what table you visited last):

Vector NTI workspace window has two toolbars which you will use extensively in these tutorials. The first is the main toolbar:

You will also use the Window toolbar extensively. It is empty to start with, but tools will appear as soon as you have at least one Display window open.

The Window toolbar is located just below the main toolbar. The Window toolbar has five different forms, for working with text, graphics, and nucleotide sequences of molecules, and for working with text descriptions and graphical displays of gels. When you are in a Display window’s text pane, the text pane toolbar will be visible. When you are in the graphics pane of a Molecule Display window, the graphics pane toolbar will be visible. The sequence pane toolbar appears when you are in the sequence pane of a Molecule Display window. The gel pane toolbar appears when you are in the gel pane of a Gel Display window.

Molecule Display window toolbar (Text pane)

Molecule Display window toolbar (Graphics pane)

Molecule Display window toolbar (Sequence pane)

Gel Display window toolbar (Text pane)

Gel Display window toolbar (Gel pane)

The Vector NTI Database Explorer window has a single toolbar.

The Explorer’s left pane shows the subbases (object subsets) of a particular table in the Vector NTI database, and the right pane shows a list of the database objects in the selected subbase. You can switch between different database tables by selecting a table from the Table menu or Table combo box in the left part of the Explorer toolbar.

The Explorer window is secondary and may be closed without exiting Vector NTI. You can activate or reopen the Database Explorer window at any time using the “Local Database” button on the main toolbar of the Vector NTI workspace.

3. Create a Display Window for pBR322

Activate the Database Explorer window and switch to the DNA/RNA molecules table. Select the DNA/RNA Molecules (MAIN) subbase and double-click on the pBR322 molecule. A Display window opens in the workspace, containing pBR322’s text description, graphical functional and restriction maps, and sequence.

4. Inspect the pBR322 Display window

The Molecule Display window has three panes, a text pane, a graphics pane, and a sequence pane. They are divided by two splitters, which you can drag with the mouse to change the relative sizes of the panes. You can press the Switch Panes button in the Window toolbar to move the keyboard input focus from pane to pane.

Study the parts of the pBR322 Display window and the information they contain:

The text pane contains folders with information about the molecule.

The graphics pane displays graphical maps of the molecule, including features and restriction sites. The features and restriction sites have labels connected to them by droplines.

The sequence pane displays pBR322's nucleotide sequence. Recognition sites of restriction endonucleases are displayed.

5. Arrange the Display window conveniently

Arrange the Display window to your liking. It can be moved within the Vector NTI workspace using standard window manipulation techniques. You can move, resize, maximize, etc. Note that the Display window has two split bars dividing the window on three panes: text description of the molecule, the graphical map, and nucleotide sequence. You can move the split bars to allow more space for any pane at the expense of other two panes.

Practice arranging the Display windows and viewing the information they provide. Then click the maximize box ( ) in the upper right corner of the window containing pBR322. The window expands to fill the entire Vector NTI workspace. Now use split bars and scroll bars to get a convenient display of pBR322’s text description and graphics map.

6. Switch to pBR322’s graphics pane

Let’s move the input focus to the graphics pane of pBR322’s Display window. First, drag the vertical split bar to the left and the horizontal split bar down until the text and sequence panes are much smaller than the graphics pane.

Now look at the Switch Panes button at the far left of the Window toolbar. The Switch Panes button tells you which pane of the Display window the input focus currently resides in, and allows you to change panes. If the switch points to the right ( ), the input focus is currently in the graphics pane. If the switch points to the middle ( ), the focus is currently in the sequence pane. If it points to the left ( ), the focus is in the text pane. When you press the Switch Panes button, the focus changes panes, and the switch on the button changes position.

Notice that when you change panes, the Window toolbar at the top of the screen changes, because you need different tools to work with graphical map and sequence than you do to work with text.

Using the Switch Panes button, move the focus to the graphics pane. We will begin exploring the graphical map.

7. Work with pBR322’s graphical map

Vector NTI allows you to freely change the size of graphical maps in the graphics pane. Clicking the tool once enlarges the image by 50%. By holding down the SHIFT key and clicking the button, you can enlarge the image in small increments. Clicking the tool reduces the image by 50%. You can reduce the image in small increments by holding down the SHIFT key and clicking the button. The button fits the image exactly to the size of the window.

Now let’s study Vector NTI’s selection techniques. In Vector NTI selection is used to define the range of a molecule’s nucleotide sequence that should serve as a parameter for a number of molecule and sequence operations (Copy Sequence, for example). One end of the selection wireframe is marked with short line called a caret. Caret is also displayed when a selection is not defined; Vector NTI uses caret position as a parameter for some molecule and sequence operations like Insert Sequence.

The simplest way to define a selection is choosing the Set Selection command from the Edit menu. Choose the command and enter the range 100bp–1000bp in the Set Selection dialog. Press the OK button. Vector NTI displays the selection with a wireframe on the graphics pane and with highlighting on a sequence pane. Notice that the current selection is also displayed as two coordinates in the selection box on the status bar. Now click on this box with the mouse. Again, the Set Selection dialog box appears. Change selection to 200bp–1200 bp.

When selection already exists, you can adjust its 5’ and 3’ ends with the mouse. Move the mouse cursor to the 5’ end of the selection wireframe. When the cursor changes its shape to the cross-hair with the 5’ mark ( ), press the mouse button and drag the 5’ end to a position near the start of the molecule (look at the selection box while you dragging). Note that Vector NTI places the caret at the end of selection you are dragging. The end of the selection marked with the caret can be moved with arrow keys on the keyboard. Press and hold the SHIFT key and use left and right arrow keys to move the 5’ end of selection one nucleotide at a time. When the 5’ end is placed on the start of the molecule (1 bp), release the SHIFT key. Now press the end key to move caret to the 3’ end of the selection. Press and hold down the SHIFT key to extend the selection and use arrow keys to move the 3’ end to 1250 bp. Now press and hold down the CONTROL key (do not release the SHIFT key) and press the left arrow key several times. Vector NTI moves the caret ten nucleotides at a time. Release the CONTROL key (do not release the SHIFT key) and press the left arrow. Notice that the caret moves one nucleotide at a time. Now release the SHIFT key and press the home key to return the caret to the 5’ end of the selection.

Now let’s start a new selection. Click anywhere in the blank area inside the molecule and drag the wireframe clockwise. Release the mouse button. Now you can use the technique described above to adjust the 5’ and 3’ ends of the selection.

Now let’s locate the TC(R) tetracycline resistance gene on the graphical map. In Chapter 7 of the Tutorial you will clone TC(R) from pBR322 into the pUC19 molecule. When you place the mouse cursor over a functional signal or its label and do not move the cursor for a short period of time, Vector NTI displays a message with information about the functional signal under the cursor. Vector NTI also changes the cursor shape to a hand ( ) to simplify selection of a signal on a graphical map. When your cursor is over TC(R), click on it once. The TC(R) signal will be selected with wireframe on the graphics pane and is highlighted on the sequence pane.

Practice selecting the parts of the molecule using the mix of the techniques described above. The general rule is that the SHIFT key should be held down to adjust the existing selection (do not press it if you want to start a new one); the CONTROL key should be held down to move the caret in larger increments with arrow keys on the keyboard.

Notice that the selected fragment is also displayed with highlighting on the sequence pane. Vector NTI always displays selection in both panes no matter which pane you used to make it.

8. Examine pBR322’s nucleotide sequence

Now that you’ve had a quick look at manipulating graphical maps with Vector NTI, let’s move on to work with pBR322’s nucleotide sequence. Drag the horizontal split bar up to get a convenient display of pBR322’s nucleotide sequence. Click anywhere in the sequence pane to activate it (the selection disappears and the blinking caret is placed at the nearest position on the sequence).

In the sequence pane, pBR322’s nucleotide sequence is displayed in blocks of ten nucleotides. This is the default block length; you can change it any time using the Display Setup command and button ( ) on the Window toolbar or through the Display Setup button in the Choose Database Molecule dialog when you open a Molecule from the database using the Open Molecule From Database command. Notice that where restriction sites occur, the name of the appropriate restriction endonuclease is shown above the nucleotide sequence, with a gray bar indicating the recognition sequence. Motifs and ORFs can also be displayed on the nucleotide sequence, by turning on those options in the Molecule Display Setup dialog. In this dialog you can also select the types and maximum length of functional signals to be displayed in a sequence pane.

You can move up and down through the nucleotide sequence using the scroll bar to the right of the sequence.

You can ask Vector NTI to translate the nucleotide sequence. Select the first few lines of the sequence by dragging the mouse from left to right along the line and then down through the sequence. The nucleotides become highlighted as you drag. You can also use SHIFT + cursor key combination to select the fragment of the sequence. Alternatively, if you know the exact coordinates of the fragment you want to select, you may use Set Selection command from the Edit menu or click on the selection box in the status bar. In any case, the selected fragment become highlighted on the sequence pane and its coordinates are displayed in the selection box in the status bar. Notice that the selected fragment is also displayed as a wireframe on the graphics pane. Vector NTI always displays the selection in both panes no matter which pane you used to make it.

When you are finished with a selection, press the Translate Direct ( ) and Translate Complementary ( ) buttons on the Window toolbar, and amino acid abbreviations appear above and below the sequence itself.

The amino acids above the sequence are the translation of the direct strand, and the amino acids below the sequence are the translation of the complementary strand. Numerals to the left of the sequence indicate the phase of the translations. For the translation of the direct strand, the phase is determined by the position of the first selected nucleotide relative to the beginning of the molecule. For the complementary strand, the phase is determined by the position of the last selected nucleotide relative to the end of the molecule. The direct strand can have phases +1, +2, or +3; the complementary strand can have phases -1, -2, or -3.

Vector NTI keeps the current sequence display settings as a part of a data set called Molecule Display Setup. Each Display window has its own Setup data set. You can change some Setup parameters directly in a Display window; others can be changed in a Display Setup dialog.

Let’s change from three-letter to one-letter amino acid codes. Press the Display Setup button ( ) on the Window toolbar and select the Display Setup command in the popup menu. The Molecule Display Setup dialog appears:

Press the Sequence Setup button in the dialog box and select 1-Letter Code option in the Sequence Setup dialog. Press OK buttons in both dialogs to return to the Molecule Display window. The proteins are now shown with one-letter amino acid codes.

Inspect the protein translations. Then press the Erase Translations tool ( ) in the Window toolbar, and the translations disappear.

9. Work with pBR322’s text description

Now let’s work with the text description of pBR322, where additional useful information is right at your fingertips. Drag the split bars until the Display window is divided evenly between all three panes.

Look at the text description of pBR322. Note that the description is made up of folders. Double-click on the General Description folder to see the name and size of the molecule and some other information. Double-click the General Description folder to close it.

Click once on the Restriction Map folder to select it, and then press the Expand Branch button ( ) in the Window toolbar.

The Restriction Map folder and all its subfolders are now open. Each subfolder contains a restriction site; the folders are in alphabetical order by name. Note that some of the folders are colored while others are grayed out. Restriction sites which are present at least once on pBR322 have active, openable folders. The deactivated folders are restriction endonucleases that were searched for but not found on the molecule or did not satisfy the search conditions (terminus type, total number of sites on the molecule, etc.). To the right of each endonuclease name is a depiction of that enzyme’s restriction site, showing its recognition sequence and cleavage points.

The current set of the restriction endonucleases searched for on the molecule is defined in the Molecule Display Setup dialog. Press the Display Setup button ( ) on the Window toolbar and choose the Display Setup command. To examine the list of selected enzymes press the RMap Setup button. The Restriction Map Setup dialog appears:

Do not change current settings for now; press the Cancel buttons in both dialogs to return to the Display window.

Locate the ApaLI folder inside the Restriction Map folder in the text pane. The folder is open, showing a list of all ApaLI sites on the pBR322 molecule. Click on the first site line to select it and press the Find button on the Window toolbar. Vector NTI selects the site on the graphics map and on the sequence. You can also use the Find button to locate functional signals, motifs, ORFs, and other objects from the text pane. The keyboard equivalent for the Find command is CONTROL+F (Windows) or COMMAND+F (Macintosh).

Close the Restriction Map folder by double-clicking it.

Now click the Functional Map folder to select it. Press the Expand Branch button ( ), and the Functional Map and all its subfolders open simultaneously. Within the Functional Map folder are subfolders containing various levels of information about the functional signals present on pBR322. We are interested in the TC(R) gene which we will be cloning into pUC19 in Chapter 7 of the Tutorial. Move through the subfolders of the functional map until you come to TC(R), in a subfolder of the CDS folder. Note that the coordinates of TC(R) are shown in its folder. The gene runs from nucleotide 86 to nucleotide 1276. Select the TC(R) folder in a text pane and press the Find button. TC(R) is selected on both graphics and sequence pane.

Now double-click on the Functional Map folder to close it.

10. Link pBR322’s text pane to the graphics and sequence panes

In Vector NTI’s Display Windows, you can link the text and graphics/sequence/gel panes so that the other panes displays only those objects whose folders are open in the text pane.

Activate the text pane and press the Link Panes button ( ) on the Window toolbar to turn on the link between the text and graphics/sequence panes. Most of the information disappears from the graphical map, leaving only the molecule name and length. The depiction of restriction sites also disappears from the sequence pane. Now let’s view a pure restriction map of pBR322. Click once on the Restriction Map folder in the text pane; this selects the folder. Then press the Expand Branch button to open all of the restriction endonuclease folders. Because the text and graphics/sequence panes are linked, the graphical map and sequence display are immediately redrawn to reflect the text pane’s open folders. pBR322’s restriction sites appear on the graphical map and on the sequence. Activate the graphics pane and press the Standard Arrangement button on the Window toolbar ( ) to arrange restriction site labels.

Now click the Functional Map folder in the text pane and press the Expand Branch button in the Window toolbar. This returns the graphics pane to a full restriction and functional map. Let’s turn off all functional signals except TC(R). One by one, close all the folders of the Functional Map except TC(R). As you close each folder, the corresponding signal disappears from the graphical map. Eventually only TC(R) is left.

Turn off the text/graphics link by again pressing the Link Panes button in the Window toolbar. The graphical map and sequence display will now return to their original state. When the panes are not linked, the graphics and sequence displays are complete and are unaffected by opening and closing text folders.

11. Print pBR322’s text description, graphical map, and sequence

To make your set of hard copies of pBR322 information, let’s print out the molecule’s text description, graphical map, and sequence. To print the text description, activate the text pane and choose the Expand All option from the View menu. Then press the Print button ( ) on the main toolbar, and all open folders in pBR322’s text description are printed out on your printer. Then, activate the graphics pane and press the Print button again. Vector NTI will print the graphical map on your printer. Now activate sequence pane and press the Print button one more time. Vector NTI will print the sequence on your printer (the pBR322’s sequence printout consists of five pages of a standard format).

12. Create a Display Window for 41BB_HUMAN

Activate the Database Explorer window and switch to the Protein Molecules table. Select the Protein Molecules (MAIN) subbase and double-click on the 41BB_HUMAN molecule. A Display window opens in the workspace, containing 41BB_HUMAN’s text description, analysis results, graphical feature map, and sequence:

_d.bmp (478726 bytes)

Double-click on the Analysis folder. You will see two tables showing the results of the automatic protein analysis. Select both tables by clicking on the Analysis folder and choosing the Select Folder command from the shortcut menu (to access a shortcut menu you should click with he right button on Windows and use COMMAND + click combination on Macintosh).

Both tables within the folder are selected. Now Press the Camera button or choose the Camera command from the Edit menu. The Camera dialog appears allowing you to choose the range and destination of your data.

If you have Microsoft Word or another RTF-capable word processor installed, you may press the Copy button, switch to the word processor program and paste the result into a new or existing document. The results will be displayed in a standard tabular form as shown here:

Analysis

Analysis	Entire Protein
Length	255 aa
Molecular Weight	27897.66 m.w.
1 microgram =	35.845 pMoles
Molar Extinction coefficient	11250
1 A[280] corr. to	2.48 mg/ml
A[280] of 1 mg/ml	0.40 AU
Isoelectric Point	8.13
Charge at pH 7	3.72

Amino Acid(s)	Number count	% by weight	% by frequency
Charged (RKHYCDE)	83	33.00	29.00
Acidic (DE)	25	10.00	9.00
Basic (KR)	29	13.00	11.00
Polar (NCQSTY)	90	32.00	31.00
Hydrophobic (AILFWV)	67	24.00	24.00
A Ala	11	3.02	4.31
C Cys	25	9.33	9.80
D Asp	11	4.51	4.31
E Glu	14	6.34	5.49
F Phe	16	8.14	6.27
G Gly	21	4.85	8.24
H His	2	0.96	0.78
I Ile	7	2.83	2.75
K Lys	13	5.85	5.10
L Leu	21	8.48	8.24
M Met	3	1.38	1.18
N Asn	12	4.88	4.71
P Pro	18	6.38	7.06
Q Gln	12	5.40	4.71
R Arg	16	8.58	6.27
S Ser	22	7.12	8.63
T Thr	17	6.24	6.67
V Val	11	3.97	4.31
W Trp	1	0.63	0.39
Y Tyr	2	1.12	0.78
B Asx	23	0.00	9.02
Z Glx	26	0.00	10.20
X Xxx	0	0.00	0.00

13. Create a Display Window for 1B14_HUMAN

Activate the Database Explorer window and switch to the Protein Molecules table. Select the Protein Molecules (MAIN) subbase and double-click on the 1B14_HUMAN molecule. A Display window opens in the workspace, containing 1B14_HUMAN’s text description, analysis results, graphical feature map, and sequence.

Arrange the panes conveniently. Notice, that this protein has a large feature map and the graphics pane appears crowded. To make it more convenient to work with, you may use the “link mode” described above. Alternatively, Vector NTI allows you to limit the view by choosing a fragment of the molecule for closer inspection.

Select the region 231 aa –276 aa using the techniques described for DNA molecules. Click on the View Molecule Fragment button and choose the View Selection (231 aa –276 aa) command from the popup menu. All three views are rearranged to display only the selected fragment. Double-click on the Analysis folder in the text pane. Notice, that the analysis tables now show values for the selected fragment as well as for the entire protein.

Most of the other techniques for manipulating Protein Molecule Display windows are exactly the same as for DNA/RNA Display windows.

14. Close the Display windows and exit Vector NTI

You have finished your first session with Vector NTI. Close Display windows using the Close command in the Molecule menu. Then quit Vector NTI with the File menu’s Exit command (Windows) or Quit command (Macintosh).

This concludes the first chapter of the Vector NTI tutorial. You have become acquainted with Molecule Display windows.