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Using Vector NTI Advance™ 10.0
Opening 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.
Vector 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.
Copy Paste
NewEdit
RenameDelete
Properties View mode
Camera Back
New subset
Database object type
Forward
List of subbases
Dismiss subset
Search
Local/Shared Data Exchange
List of database
records
Figure 2. Vector NTI Explorer Window
Figure 3. List of object types.
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
View Molecule Fragment
Display Setup
Sequence Pane
Text Pane
Graphics Pane
Figure 5. Pane-specific
Add to Oligo list
Delete Annotation
Collapse Branch
Expand Branch
Find
Link Panes
Expand Folder
Figure 6. Text Pane
Add Feature
Graphics Display Setup
Find
Circular Display
Linear Display
Zoom In
Add Annotation
Edit Picture
Translate Complementary
Translate Direct
Standard Arrangement
Fit to Window
Zoom Out
Figure 7. Graphics Pane
Graphics Display Setup
Add Feature
Cut
Copy
Paste
Show Both Strands
Italic Underline
Font Size
Font Color
Background Font Color
Font Name
Bold
Erase Translations
Translate Complementary
Translate Direct
Figure 8. Sequence pane
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.
7. Create a new Subset Name and click OK.
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.
8. On General page, create the name of vector in this box.
• 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 Edit sequence…to add the nucleotide sequences.
4. Paste nucleotide sequences in this area.
5. Click OK to create new molecule.
2. On General page, create the name of vector in this box.
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.
Show the information of each feature in the Feature Map.
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
5. Click OK.
4. Change Font, Font style, Size and Color of Font, click Font…
3. To modify a feature, click More…
9. Click OK to close the dialog box. 7. On the Fill page, select a
color from the color menu.
6. To change the Symbol style, click the More…
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.
4. On the Shape page, select a shape from the shape menu.
5. Click OK. to close the dialog box.
Show the result.
Generating 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.
Show the NdeI restriction enzyme
that you chose
3. Click <Add… to choose the restriction enzyme.
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.
Restriction site is shown on the Sequence pane.
Display the Restriction Map within the molecule on the Graphic Pane.
Show the information of each restriction enzyme in the Restriction Map.
Primers 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.
1. Open DNA template file from the Local Database.
3. Select Analyses > Primer Design > Find PCR Primers…to open the Find Primers in Selected Region of DNA template dialog box.
4. Edit the Product Length (for example, up to maximum).
2. Choose the gene of interest to design primers.
5. Click More >> to attach to 5’terminus of primers.
6. Click … to open the Choose Database Enzyme dialog box.
7. Choose the restriction enzyme to design Sense Primer and Antisense Primer and then click OK.
8. Click OK to close the box.
10. Select View> PCR Product > Save All PCR Products to Database…to enter the prefix for PCR Product(s) name(s) box.
Vector NTI generates a number of primer options that satisfy the conditions previously defined in the PCR Analysis.
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.
The Sequence of PCR product is displayed on Sequence Pane.
The PCR product is displayed on Graphics Pane.
Show the information of each primer in the Feature Map > Primer.
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.
• Define the First Fragment.
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.
7. Define the 3’ terminus of the new fragment, hold down the SHIFT key and click on the restriction site label in the Graphics Pane and click the Finish in this screen to complete the definition of the fragment.
6. Define the 5’ terminus of the new fragment, click on the restriction site label in the Graphics Pane and click the Next> in the dialog box to proceed.
8. Click the Add to List to add the first fragment to the list.
• Define the Second Fragment.
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.
11. Define the 5’ terminus, click on the restriction site label in the Graphics Pane and click the Next> in the dialog box to proceed.
13. Click the Add to List to add the second fragment to the list.
12. Define the 3’ terminus, hold down the SHIFT key and click on the restriction site label in the Graphics Pane and click the Finish in this screen to complete the definition of the fragment.
15. Click Run to create the new DNA molecules. 14. Select the two fragments.
17. Check this part to create all possible constructs with compatible fragment.
18. Click Construct to create the new DNA molecules.
16. Create the name of the construct molecules.
20. Click Yes to create constructs.
19. Insert the molecule into subset in the Local Database and click OK.
The two fragments that you used to make this molecule are listed in the Component Fragments. Their subfolders describe the left and right termini of each fragment.
The new molecule is displayed and changed graphic display on the Graphics Pane.
