Using Vector Nti Advance 10.0
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Using Vector NTI Advance™ 10.0 ¾ 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.
¾ 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: • •
), or In the Molecule Viewer, click on the Local Database icon ( From the Windows® Start menu, select Programs > > Invitrogen > Vector NTI Advance 10 > Vector NTI Explorer.
Local/Shared Data Exchange Search Dismiss subset New subset Forward
Copy Paste New Edit Rename Delete Properties View mode
Back
Camera
List of subbases Database object type
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 ( 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
Graphics Pane
Sequence Pane
Text Pane
Display Setup View Molecule Fragment
Figure 5. Pane-specific
) on
Expand Branch Collapse Branch
Expand Folder
Delete Annotation
Link Panes
Add to Oligo list
Find
Figure 6. Text Pane
Zoom In
Zoom Out
Linear Display
Fit to Window Standard Arrangement
Circular Display
Translate Direct
Find
Translate Complementary
Graphics Display Setup
Edit Picture
Add Feature
Add Annotation
Figure 7. Graphics Pane Show Both Strands Paste Copy Cut
Translate Direct Translate Complementary Erase Translations Bold Italic
Graphics Display Setup
Underline Font Size
Add Feature
Font Name
Figure 8. Sequence pane
Background Font Color Font Color
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…
4. Import molecules from GenBank/GenPept, EMBL/SWISS-PROT and FASTA formats.
5. Click OK.
6. Choose the file that you want to import and click Open.
7. Create a new Subset Name and click OK.
8. On General page, create the name of vector in this box.
9. Select the molecule type on DNA/RNA molecule page and click OK.
10. Double click the created file to open.
11. The result is showed in Molecule Viewer.
•
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.
2. On General page, create the name of vector in this box.
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.
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 the information of each feature in the Feature Map.
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 ( the main toolbar.
2. Click Graphics Display Setup.
) on
1. Select the feature that you want to change the graphics display.
Show the Feature type
3. To modify a feature, click More…
4. Change Font, Font style, Size and Color of Font, click Font…
5. Click OK.
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.
2. Select the feature that you want to change the graphics display and right click to choose Properties.
3. On the Fill page, select a color from the color menu.
5. Click OK. to close the dialog box. 4. On the Shape page, select a shape from the shape menu.
Show the result.
¾ 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 ( Display Setup dialog box.
) on the main toolbar to open the Molecule
1. Click Display Setup.
2. Select RMap Setup… to open Restriction Map Setup dialog box. 3. Click
5. Click OK rel="nofollow"> OK to close the dialog box. Show the NdeI restriction enzyme that you chose
Show the information of each restriction enzyme in the Restriction Map.
Display the Restriction Map within the molecule on the Graphic Pane.
Restriction site is shown on the Sequence pane.
¾ 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. 3. Select Analyses > Primer Design > Find PCR Primers…to open the Find Primers in Selected Region of DNA template dialog box. 1. Open DNA template file from the Local Database.
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.
7. Choose the restriction enzyme to design Sense Primer and Antisense Primer and then click OK.
6. Click … to open the Choose Database Enzyme dialog box.
8. Click OK to close the box.
Vector NTI generates a number of primer options that satisfy the conditions previously defined in the PCR Analysis. 10. Select View> PCR Product > Save All PCR Products to Database…to enter the prefix for PCR Product(s) name(s) 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.
Show the information of each primer in the Feature Map > Primer.
The PCR product is displayed on Graphics Pane.
The Sequence of PCR product is displayed on Sequence Pane.
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.
•
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.
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.
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.
8. Click the Add to List to add the first fragment to the list.
•
Define the Second Fragment.
9. Press Add > Add Fragment > of the name of the molecule of interest (Second Fragment) to open the Fragment Wizard dialog box.
10. Select the Construction Fragment option, choose the Insert Inverted option checked, and click the Next> to proceed.
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.
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.
13. Click the Add to List to add the second fragment to the list.
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.
Molecule Viewer
Vector NTI Explorer
Figure 1. Opening the Molecule Viewer and Vector NTI Explorer.
¾ 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: • •
), or In the Molecule Viewer, click on the Local Database icon ( From the Windows® Start menu, select Programs > > Invitrogen > Vector NTI Advance 10 > Vector NTI Explorer.
Local/Shared Data Exchange Search Dismiss subset New subset Forward
Copy Paste New Edit Rename Delete Properties View mode
Back
Camera
List of subbases Database object type
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 ( 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
Graphics Pane
Sequence Pane
Text Pane
Display Setup View Molecule Fragment
Figure 5. Pane-specific
) on
Expand Branch Collapse Branch
Expand Folder
Delete Annotation
Link Panes
Add to Oligo list
Find
Figure 6. Text Pane
Zoom In
Zoom Out
Linear Display
Fit to Window Standard Arrangement
Circular Display
Translate Direct
Find
Translate Complementary
Graphics Display Setup
Edit Picture
Add Feature
Add Annotation
Figure 7. Graphics Pane Show Both Strands Paste Copy Cut
Translate Direct Translate Complementary Erase Translations Bold Italic
Graphics Display Setup
Underline Font Size
Add Feature
Font Name
Figure 8. Sequence pane
Background Font Color Font Color
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…
4. Import molecules from GenBank/GenPept, EMBL/SWISS-PROT and FASTA formats.
5. Click OK.
6. Choose the file that you want to import and click Open.
7. Create a new Subset Name and click OK.
8. On General page, create the name of vector in this box.
9. Select the molecule type on DNA/RNA molecule page and click OK.
10. Double click the created file to open.
11. The result is showed in Molecule Viewer.
•
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.
2. On General page, create the name of vector in this box.
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.
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 the information of each feature in the Feature Map.
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 ( the main toolbar.
2. Click Graphics Display Setup.
) on
1. Select the feature that you want to change the graphics display.
Show the Feature type
3. To modify a feature, click More…
4. Change Font, Font style, Size and Color of Font, click Font…
5. Click OK.
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.
2. Select the feature that you want to change the graphics display and right click to choose Properties.
3. On the Fill page, select a color from the color menu.
5. Click OK. to close the dialog box. 4. On the Shape page, select a shape from the shape menu.
Show the result.
¾ 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 ( Display Setup dialog box.
) on the main toolbar to open the Molecule
1. Click Display Setup.
2. Select RMap Setup… to open Restriction Map Setup dialog box. 3. Click
5. Click OK rel="nofollow"> OK to close the dialog box. Show the NdeI restriction enzyme that you chose
Show the information of each restriction enzyme in the Restriction Map.
Display the Restriction Map within the molecule on the Graphic Pane.
Restriction site is shown on the Sequence pane.
¾ 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. 3. Select Analyses > Primer Design > Find PCR Primers…to open the Find Primers in Selected Region of DNA template dialog box. 1. Open DNA template file from the Local Database.
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.
7. Choose the restriction enzyme to design Sense Primer and Antisense Primer and then click OK.
6. Click … to open the Choose Database Enzyme dialog box.
8. Click OK to close the box.
Vector NTI generates a number of primer options that satisfy the conditions previously defined in the PCR Analysis. 10. Select View> PCR Product > Save All PCR Products to Database…to enter the prefix for PCR Product(s) name(s) 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.
Show the information of each primer in the Feature Map > Primer.
The PCR product is displayed on Graphics Pane.
The Sequence of PCR product is displayed on Sequence Pane.
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.
•
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.
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.
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.
8. Click the Add to List to add the first fragment to the list.
•
Define the Second Fragment.
9. Press Add > Add Fragment > of the name of the molecule of interest (Second Fragment) to open the Fragment Wizard dialog box.
10. Select the Construction Fragment option, choose the Insert Inverted option checked, and click the Next> to proceed.
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.
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.
13. Click the Add to List to add the second fragment to the list.
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.
