vector protocaol说明书

Using Vector NTI Advance™ 10.0
¾Opening Vector NTI Advance™ 10.0
1. On your Windows® desktop, click on the Start button.
2. Select Programs > Invitrogen > Vector NTI Advance 10 to open the menu of
Vector NTI Advance™ modules.
3. Select Vector NTI Explorer to open the Explorer or Vector NTI to open the
Molecule Viewer,as shown in Figure 1.
Molecule Viewer
Vector NTI Explorer Figure 1. Opening the Molecule Viewer and Vector NTI Explorer.
¾Vector NTI Explorer
Vector NTI Explorer is the main tool for accessing the information in your local Vector NTI Advance™ database. Using the Explorer, you can import, open, export, and organize molecules and other database items, and launch other Vector NTI Advance™ modules (Figure 2). To launch Vector NTI Explorer:
• In the Molecule Viewer, click on the Local Database icon
(), or
• From the Windows®Start menu, select Programs > > Invitrogen > Vector NTI Advance 10 > Vector NTI Explorer.
Local/Shared
Data Exchange
List of
database
records
Figure 2. Vector NTI Explorer Window
Figure 3. List of object types.
¾ Molecule Viewer
The Molecule Viewer displays information about DNA, RNA, and protein molecules. To
launch the Molecule Viewer :
• From the Windows® Start menu , select Programs > Invitrogen> Vector NTI
Advance 10 > Vector NTI , or
• Double-click on a molecule name in the Vector NTI Explorer . To open a molecule from within the Molecule Viewer , click on the Open button
(
) on
the main toolbar and select the molecule name from the dialog box.
The molecule will be loaded into the Molecule Viewer .
Pane-specific Graphics Pane
Text Pane (info about features, restriction site, etc.) Sequence Pane
Figure 4. Molecule Viewer window
Text Pane Graphics Pane
Figure 5. Pane-specific
Figure 6. Text Pane
Figure 7. Graphics Pane
Figure 8. Sequence pane
¾ Create a Molecule Display Window
There are 2 different ways of creating new DNA/RNA in Vector NTI:
• Importing from GenBank/GenPept, EMBL/SWISS-PROT and FASTA formats .
The sequence and Feature map are converted from the file, and the new
molecule becomes part of the Vector NTI database.
1. Open the Vector NTI Explorer.
2. Select the
DNA/RNA Molecules
(Main) within the database table combo box.
3. Select the Import
and click the Molecule
from Text file…
5. Click OK.
4. Import molecules from GenBank/GenPept, EMBL/SWISS-PROT and FASTA formats.
6. Choose the file that you want to import and click Open.
10. Double click the created file to open. 11. The result is showed in Molecule Viewer. 9. Select the molecule type on DNA/RNA molecule page and click OK.
•
Creating new molecules from user-defined nucleotide sequences. These can be manually entered or pasted from the clipboard and the sequence entered as a new molecule.
1. Open File > Create New Sequence >
Using Sequence Editor (DNA/RNA)… within the Molecule Viewer.
3. On Sequence and Maps , click sequence…to add the nucleotide sequences.
¾ Working with a Molecule’s Graphical Representation
Vector NTI also lets you manually format graphical maps and change the predefined display style for elements of feature and restriction maps. You can also change the shape and drawing style of features, move and format text, add text annotations, etc.
A. Add features within molecule
1. Select Graphics Pane.
2. Click Add Feature.
3. Choose the Feature.
4. Create the Feature Name.
5. Add the Position of Feature.
6. Select Complementary when you want to change the direction of the feature in the molecule.
7. Click OK.
Show graphical maps in the Graphics Pane.
B. Change the Graphics Display
There are 2 different ways of Change the Graphics Display in Vector NTI:
•Change the Graphics Display, click on the Graphics Display Setup ( ) on the main toolbar.
1. Select the feature that you want to
change the graphics display.
2. Click Graphics Display Setup.
Show the
Feature type
8. Click OK.
• The other way, click on the Edit Picture () on the main toolbar.
1. Click Edit Picture.
3. On the Fill page , select a color from the color menu. 2. Select the feature that you want to change the graphics display and right click to choose Properties.
5. Click OK. to close the dialog box.
Show the result.
¾Generating Restriction Maps
Restriction maps of DNA/RNA molecules can be quickly generated in Vector NTI. For unsequenced molecule regions, you may enter the known positions of restriction sites. All the molecule descendants inherit these sites.
There are 2 different ways of Generating Restriction Maps in Vector NTI:
•Generating Restriction Maps, select Analyses > Restriction Analyses > Restriction Site…to open the Restriction Map Setup dialog box.
•
Click on the Display Setup () on the main toolbar to open the Molecule
Display Setup dialog box.
2. Select RMap Setup… to open Restriction Map Setup dialog box. 1. Click Display Setup .
4. Choose the restriction enzyme and click OK.
5. Click OK > OK to close the dialog box.
Display the Restriction Map
within the molecule on the
Graphic Pane.
Restriction site is shown
on the Sequence pane.
¾Primers Design and PCR Analysis
Vector NTI can design PCR primers, sequencing primers and hybridization probes and save them to the database for future use. Using parameters you have defined, Vector NTI
can analyze those primers and probes or those you have defined yourself to determine the
best ones for optimal experimental results.
4. Edit the Product Length
(for example, up to maximum).
to open the Choose Database Enzyme dialog box.
8. Click OK to close the box.
9. Highlight the PCR product.
11. Create the PCR product name. 12. Click OK .
13. Insert the molecule into subset in the Local Database and click OK .
14. Open the Local Database.
15. Double click this file to open
on Molcule Viewer.
¾ Molecule Construction
Construction means creating a DNA molecule from fragments that are completely defined and made compatible by the user.
1. Open the first fragment from Local Database.
2. Then open the second molecule from Local Database again.
Two display windows are now open.
3. Select List
> Show Lists to open the Lists
dialog box.
4. Press Add > Add Fragment > of the name of the molecule of interest (First Fragment) to open the Fragment Wizard dialog box.
5. Select the
Construction Fragment option, leave the Insert Inverted option unchecked and click the Next > to proceed.
8. Click the Add to List to add the first fragment to the list.
10. Select the Construction Fragment option, choose the Insert Inverted option checked, and click the Next>
to proceed. 9. Press Add > Add Fragment > of the name of the molecule of interest (Second Fragment) to open the Fragment Wizard
dialog box.
15. Click Run to create the new DNA molecules.
20. Click Yes to create constructs.。