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Advanced Workshops on Vector NTI
Part I – Managing Vector NTI Database
Yi-Bu Chen, Ph.D.
Ansuman Chattopadhyay, Ph.D.
Health Sciences Library System
Molecular Biology and Genetics Information Service
University of Pittsburgh
Overview of the Workshop
A. Navigate the Vector NTI Database Explorer
B. Menu and Toolbar Comments
C. Create New Database Subsets
D. Edit or add new user-fields to database objects
E. Search and report database objects
F. Backup and archive databases
G. Import, export, migrate databases
H. Hands on Exercises
The Vector NTI Database Explorer
Navigate the Database Explorer: Tables
 DNA/RNA Molecule Table – Stores DNA and RNA Molecules,
including constructed and designed molecules.
 Protein Molecules Table – Stores Protein Molecules.
 Enzymes Table – Stores restriction enzymes.
 Oligos Table – Stores oligonucleotides up to 1000 bases in length.
 Gel Markers Table – Stores gel markers that can be used in Vector
NTI’s simulated electrophoresis.
 Citations Table – Stores citations retrieved through the Vector NTI
PubMed Search engine, from the NCBI website or from other searches. It
provides complete bibliographic conversion features.
 BLAST Results – Stores independent of molecules in a BLAST Results
database.
 Analysis Results – Stores results from various analysis, such as PCR
analysis, PFAM analyses, etc.
Navigate the Database Explorer: Panes and View Options
 Subset Pane – Displays the subsets for the selected table.
 Database Objects Pane – Displays the contents of a subset.
 View Options – Choose from “large icons, small icons, list and
details”.
☺MENU > View > ; OR Right click on mouse > Select the desired option
 Arrange and Sort Database Objects – Arrange command
designates a column to be sorted; Sort command allows either
ascending or descending.
☺ MENU > Arrange; OR right click on mouse > Arrange Icons
Navigate the Database Explorer: More View Options
 Edit and Arrange Column List – Customize the columns and
their layout in the Database Objects Pane.
☺Move mouse cursor on any
column name > Right click on
mouse > Columns > Open the
Options dialog window >
customize the column selections
and layout.
☺OR Menu|View > Options >
“Details View Tab”
Note: The Options dialog window
also allows configuration of
default settings for a few other
commands.
Menu, Toolbar Commands and Selections
 Menu/Toolbars – Notice the switch between the panes.
 Popular Toolbar
-- Create a new subset
-- Remove a subset without affecting the database objects.
-- Search database objects.
-- Rename a subset or database object.
 Selecting multiple database objects
☺ SHIFT + CLICK to select all objects within a range
☺ CTRL + CLICK to select non-contiguous objects in a list
☺ “Wire-frame” selection (press the mouse button somewhere outside
item names/icons and drag the selection rectangle)
Creating A New Database Subset
1. Select Table > New > Subset OR click the New Subset
button to create a new (empty) subset with a default
name, Group 1. The default name can be changed
later.
2. Select Table > New > Subset (using Subset Editor) to
create a new subset and select its contents in the Edit
Subset dialog window.
3. To create a new subset and place objects in it at the
same time:
> Select objects for the new subset in the Database
Objects Pane > click the New Subset button > use the
default name or enter a new name.
Adding or Removing Objects from A Database Subset
 The simple way of adding  Open the source subset in the
Subset Pane > Select and drag selected objects from the list to
the new subset.
 Add or remove objects from a subset
Select the subset > Menu|Table > Edit Subset > Make
selections in the Editing Subset dialog window.
Editing A Database Subset
 Dismiss a subset
Select the subset > Menu|Table > Dismiss Subset, OR click the Dismiss Subset
button. This operation removes a selected subset, but DOES NOT affect the
database objects.
 Clear a subset
Select the subset > Menu|Table > Table > Clear Subset to exclude all objects from
the selected subset. The subset itself is emptied but not removed. This operation
DOES NOT affect database objects.
 Delete content of a subset
Select the subset > Menu|Table > Delete Contents from Database to physically
delete from the database all objects of the specified subset. The objects in the subset
are permanently deleted from the Vector NTI database, and the subset itself is
removed.
 Rename a subset
Select the subset > Menu|Table > Rename Subset OR click the Rename button.
 OR: Mouse click right button
All above operations can be done by clicking the right mouse button while the
desired subset is selected > then choose desire actions from the menu.
Editing a Subset Based on the Existing Subsets
In the Subset Pane, select the subset > Menu|Table|Edit Subset > In the Editing subset
dialog box, select all desired source subsets in the Source Subsets column > Configure
criteria (Intersection, Difference, Union) for the desired Source Content > Select the
desired molecules in the Source Content column > Click Add button to add desired
molecules to the Resulting Content column, which represents the subset being edited.
> Click OK button to complete the editing.
 Intersection – Only molecules presented in ALL selected Source Subsets are displayed in the
Source Content column.
 Difference – Only molecules presented in ONE of the selected Source Subsets are displayed.
 Union – ALL molecules in the selected Source Subsets are displayed.
Import Molecules into a Database Subset
 Drag and Drop Import
In Windows Explorer, select molecule(s) from text files/or a folder containing the
files > Drag and drop the selections onto the desired subset in Vector NTI Explorer.
(Exercise: drag and drop nm_002660.gb and nm_002660-fasta.txt into a subset from the “Vector NTI
workshop” folder on the desktop.)
 Import using menu options > Select Menu|Table > Import, select one of the
following options:
1. Import Molecule From Text File – imports DNA/RNA/protein molecule data.
Accepted format: GenBank/GenPept, EMBL/SWISS-PROT, and FASTA files.
2. Import Sequence From Text File – imports a nucleotide or amino acid
sequence text file, creating a new DNA/RNA/protein molecule with the sequence.
Accepted format: ASCII format text files.
3. Import Molecules From Archive – imports objects from a Vector NTI archive.
Accepted format: Vector NTI archive .mr format.
4. Import Molecules From Directory of Text Files (molecules and oligos only)
Accepted format: GenBank (DNA/RNA), GenPept (protein) or Vector NTI’s oligo
text format (oligonucleotides).
Batch Import Molecules into a Database Subset
1. Create a text file containing multiple molecules
Use Notepad or MS Word to create a file contains multiple sequences from your
source; make sure that each sequence is separated by blank lines; make sure all
sequences are in the same format (anyone of the accepted format); save the
sequence file as a .txt file
Accepted format: GenBank/GenPept, EMBL/SWISS-PROT, and FASTA files.
2. Import Multiple Sequences From the Text File
►In Vector NTI Database Explorer, select the appropriate Table
►Create a new subset to store the molecules to be imported
►Open Windows Explorer, locate the file containing the multiple sequences; >
Drag and drop the file into the newly created subset in Vector NTI Explorer
►The multiple sequences in the sequence file will be converted to multiple
individual molecule file in the selected subset, with each molecule file corresponds to
each sequence in the original sequence file.
(Exercise: drag and drop 2 genes-fasta.txt and 2 genes-genbank format.txt into a subset from the “Vector
NTI workshop” folder on the desktop.)
Export a Subset
 Export subset into a Vector NTI Archive
Select Menu|Table > Export > Subset into Archive to export all
objects of the specified subset to a VNTI archive > In the Write
To dialog box, indicate the directory or folder, and file name
for archive storage > Click the Save button.
 Export All subset objects into a directory of text files
(molecules and oligos only)
Select Menu|Table > Export > Subset to Directory of Text Files
to export all objects of the specified subset into a directory of
text files in GenBank (DNA/RNA molecules), GenPept (protein
molecules) or Vector NTI’s oligo text format (oligonucleotides)
> In the dialog box, browse for the location and enter the file
name under which the subset is to be stored.
Important Operations on Database Objects
Most of the commands below are applicable to all database objects, and many
can be accessed from the short cut menu or the toolbars (OR right mouse click
while pointing at a database object).
1. Open – opens selected objects; available only for DNA/RNA/protein molecules.
2. Edit – modify user fields, comments, keywords, etc. for an object selected in the
Database Objects Pane. This command is enabled only with a single selected object.
You can also use the Edit button.
3. Exclude from a subset – removes the selected objects from current subset. The
objects are still stored in the database and are included in all other subsets where they
were included before this operation.
4. Delete from the database – physically deletes the selected object from the entire
database. If a DNA molecule is deleted, Vector NTI scans all its descendants and
disconnects them from the deleted molecule.
5. Export – allows to export molecules or sequence to text files (for DNA/RNA/protein
objects); or export any selected objects to an archive.
6. Report – Produce a report for selected DNA/RNA/protein molecules. Very useful for
lab documentation.
Basic Steps for Database Search
The Database Explorer allows sophisticated search by different
criteria to locate any object in the database.
1. Select a desired database table – Any searches are confined within a specific type
of database objects, one must specify a database type before the search.
2. Select filters – Menu|Database > Search OR Click the Search button > in the
Database Search Dialog Box, check the boxes for desired filters.
Basic Steps for Database Search—Continued
3. Define filters – Open the Filter Setup Dialog Box for desired filters and further
configure the filters. When multiple filters are checked, a search that satisfies all the
search criteria (an AND search) will be performed. Check ONLY the filter(s) that you
want to include into the search.
4. Start search – Inspect the final configuration of the Search Database Dialog Box >
Click Start Search button.
5. Save the search results – when the search is finished, the Insert Search Results into
Subset dialog box will appear > select an existing subset and Vector NTI will remove all
existing contents in that subset before placing the search results into it; OR Enter a new
name for the subset and all the search results will be saved to this new subset.
Configure the Database Search Filters —
the Attribute Filters for DNA/RNA/Protein Molecules
Configure the Database Search Filters — the Text Filter
 The Text Filter enables text search from selected field(s).
 Users can use the Text Filter to search for the database objects containing
desired author names, organisms names, and other textual information.
 Select only the fields where the desired text should occur.
Example:
Search all molecules
created by yibu:
Text filter > check
Author field > type
“yibu” in “New
substring” field >
Click Add button > Ok
button
Start Search > save the
search results in a new
subset yibu.
Configure the Database Search Filters — the Keyword Filter
 The Keyword Filter enables text search ONLY in the Keyword field.
 Keywords can be entered by editing the existing objects, or when a new
object is created.
 Keywords search are very helpful for locating specific objects in a large
database. Always enter keywords when you create a new object so you can
find it easily later on.
 Popular keywords: user’s last name, organism name, gene name, project
name, etc.
Configure the Database Search Filters — the Ancestors Filter
 The Ancestors Filter allows user to find molecules that have
specified ancestor(s) molecules.
 The Ancestors Filter is useful for finding constructed or
designed molecules.
Configure the Database Search Filters
— the Oligo & Peptides Filter
 The Oligo & Peptides Filter allows user to find molecules that are similar to
the sequences of the specified Oligo/peptides.
 Click the Add Oligo or Add Peptide button > in the subsequent dialog box,
enter the oligos from the existing oligo database by clicking the Oligo
Database, OR enter new oligo or peptide by clicking the Add New… button.
 Select the desired genetic code to be used for the search from the Genetic
Code drop-down box. Automatic translation/back translation is carried out
whenever needed.
Configure the Database Search Filters
— the Features Filter
 The Features Filter allows user to find molecules with specific
features.
 Click the <Add… button > in the subsequent dialog box, select
desired feature type and then one or multiple features within
the group > Click the OK button to complete the filter setup.
 Feature types differ for DNA/RNA searches and protein
searches.
Configure the Enzyme Database Search
1. Recognition String Filter – Enter a nucleotide string that must be found in the
recognition site of the desired enzyme.
2. Attributes Filter – Specify enzyme attributes necessary for the search.
“Ambiguous” recognition site – the site containing any nucleotide besides A, T, G, or C.
3. Text Filter – Filter search results based on text in various object fields.
4. Keyword Filter – Filter search results based on keywords.
Configure the Oligo Database Search
1. Nucleotide String Filter – Enter a Nucleotide String filter that must be found in the
sequence of the desired enzyme and select the strand to search, direct or complementary.
2. Attributes Filter – Check to limit the search space to gel markers with specified
length of the longest fragment. If all are checked or unchecked, the filter has no effect.
3. Text Filter – Filter search results based on text inside various object fields.
4. Keyword Filter – Filter search results based on keywords.
Configure the Gel Marker Database Search
Gel Markers are sets of fragments of known sizes. They are used as standards
for measuring migration speed in Vector NTI simulated electrophoresis.
1. Attributes Filter – Check to limit the search space to gel markers with specified
length of the longest fragment. If all are checked or unchecked, the filter has no effect..
2. Text Filter – Filter search results based on text inside various object fields.
3. Keyword Filter – Filter search results based on keywords.
Configure the Citation Database Search
The Citation Database Search allows users to search citations by
Citation, Text, and/or Keywords.
Using the Vector NTI Citation Database
Users can use the Citation Table to generate references list for a manuscript just
like what they can do with reference software, such as Endnote.
 Formatting Bibliographic References embedded in a document
1. Tag the reference – In Citation Table > Select desired reference >
Menu|Citation|Copy Tag > Paste the tag in your document opened with a word
processor. Save your document as a Rich Text Format file when done.
2. Generate the references – In Citation Table > Menu|Citation|Format Manuscript >
in the Format manuscript dialog box, click Browse button to select the RTF document >
in the Format reference for drop down menu, select a desired journal name > Click
Start button > the tagged the document will be formatted with proper citations and
bibliographies.
Using the Vector NTI Citation Database -- continued
Users can also use the Citation Table to copy selected references in desired
journal format for later use.
 Copy Selected References
1. Select desired references – In Citation Table > Select desired references with Ctrl +
left mouse click
2. Generate the references – In Citation Table > Menu|Citation|Copy Bibliography >
In the Copy Bibliography dialog box, select the journal whose formatting the
bibliography should follow > click OK button.
3. Save the references – Open your word processing document and paste the
formatted citations.
Vector NTI Database Maintenance
1. Database Backup
Backing up your database is extremely important. It should be performed at least
every month, but a weekly backup is recommended. Backups should be stored on both
the hard drive and a removable media, such as a CD.
– Menu|Database > Database Backup > in the Choose Backup Directory dialog box,
select an existing folder OR create a new folder to store the backup.
Note: Vector NTI Database Backups are NOT cross-platform compatible (i.e. the Vector
NTI Database on a PC cannot be restored using a VNTI Database Backup made from
Vector NTI on a Macintosh, and vice versa. For cross-platform backup/restore, users
must use VNTI Archive command with each subset (Export and Import command).
2. Database Restore
This operation restores ALL database files from a specified backup.
– Menu|Database > Database Restore > in the Choose Backup Directory dialog box,
select the directory where the last backup was stored > the database will be restored.
Warning: the restored database will overwrite all current database files.
3. Database Cleanup
This operation removes accumulated “junk” data. It may also be used to recover lost
or damaged files or tables. The cleanup should be performed on monthly basis.
– Menu|Database > Database Cleanup.
Vector NTI Database Migration Strategies
1. Moving/copying entire database from PC to PC
From Version 9.0 or later to Version 10
> Copy the entire database folder in the source PC (200-500 MB) > Move the source folder to the
hard drive of the target PC > Open ONLY the Vector NTI Database Explorer on the target PC >
set the local database by Menu|Database|Select local database > navigate to locate the database
folder > the Vector NTI Database Explorer will restart to take the newly selected database as the
default database.
Note: this is the BEST strategy as it moves everything (data and program settings) without too much
efforts.
From Version older than 9.0 – same as the strategy used for moving between PC and
MAC as described below.
2. Moving/copying entire database between PC and MAC
> Archive each subset of each database table from the source computer > Import each archived
file using Vector NTI Database Explorer on the target computer.
Note: This strategy requires some efforts, but it ensures that all subsets will be correctly moved
between different platform or between old and new version of Vector NTI.
3. Copy entire database using the database backup function or Vector NTI Database
Migration Utility
These two methods are NOT recommended as they only move data (molecules, enzymes
etc) but not subset information.
Vector NTI Database Management Workshop
Exercise 1 – Edit A Molecule Object
 Modify a DNA molecule CREB1 by adding your last name to
the keyword field, and generate a report about this molecule.
 The answer key
1.
Select the DNA/RNA Molecule Table > Sort the name column to locate
CREB1 molecule > click right mouse button > Edit.
2.
In the Edit CREB1 dialog box > browse all the tabs > under the keywords
tab, enter your last name and click Add. Note the Author change for
CREB1.
3.
Click right mouse button on CREB1 > Report|General > In Select Report
Type dialog box, select New Report > In Molecular Display Setup dialog
box, select Default > Browse the options in the Set General Report
Options > Browse the feature options in the Set Feature Map Options
dialog box > Click Finish button > Print the report, or Click Camera
button > in the Camera dialog box, make desired selection and copy-to
destination. The contents can be pasted to a word processor.
Vector NTI Database Management Workshop
Exercise 2 – Create a new subset
 Create a new subset (subset name: “your last name-kinase”)
which consists protein kinase molecules with a size between
500-1500 amino acid residues.
 The answer key
1.
Select the Protein Molecule Table > Click on the Search Database Button.
2.
Configure the search criteria: Check the Text Filter > Set up the search
for “kinase” in the Description Field > Check the Attribute Filter > Check
the size “500 aa -1500 aa” > Click Start Search Button
3.
Save the search results to a new subset: In the Insert search results into
subset dialog box, enter the new subset name > Click Ok button.
Vector NTI Database Management Workshop
Exercise 3 – Search and Create a new subset
 Search the existing protein molecules database to find all
Transmembrane proteins and store them in a new subset
 The answer key
1.
Select the Protein Molecule Table > Click on the Search Database Button.
2.
Configure the search criteria: Check the Feature Filter > Click Add > In
the Add Features dialog Window, locate the “Transmembrane” feature
under the Protein Functional Features > Domains> Check Add all features
of this type > Click OK > Click OK > Click Start Search
3.
Save the search results to a new subset: In the Insert search results into
subset dialog box, enter the new subset name > Click Ok.
Vector NTI Database Management Workshop
Exercise 4 – Archive/Export a subset
 Archive and export the newly created subset.
 The answer key
1. Export a Subset:
Select the newly created subset > Menu|Table|Export|Subset into a
directory of text file > in Export Protein To dialog box, create a new folder
on the desktop and enter the subset name as the file name, click OK > all
molecules in the new subset are now exported into the directory.
2. Archive a Subset:
Select the newly created subset > Menu|Table|Export|Subset into Archive >
in Write Proteins To dialog box, enter the subset name as the archive file
name and select the desktop as the destination, click Save button > a single
archive file is created.
3. Delete the newly created subset: > Select the subset in the Subset Pane >
Table|Delete Contents from Database > Table|Dismiss Subset
Vector NTI Database Management Workshop
Exercise 5 – Import Molecules
 Import protein molecules from the archive file and the directory of text
files created from the previous exercise. The imported molecules are to be
stored in new subsets (name your own).
 The answer key
1. Import molecules from a directory of text files:
Select the proper database table, Menu|Table|Protein Molecules >
Menu|Table|Import|Molecules from Directory of Text Files > in the Import Proteins
dialog box, locate the folder, and select the protein list file (.pls file) > click Open >
in the Insert Protein Molecules into Subset dialog box, enter the name for the new
subset > click OK, and all the molecules in the directory are now successfully
imported into the new subset.
2. Import molecules from an archive file:
Select the proper database table, Menu|Table|Protein Molecules >
Menu|Table|Import|Molecules from Archive > in the Import Protein Archive From
dialog box, locate the protein archive file (.pa4 file), click Open > in the Insert
Protein Molecules into Subset dialog box, enter the name for the new subset > click
OK, and all the molecules in the archive file are successfully imported into the new
subset.
Vector NTI Database Management Workshop
Exercise 6 – Database Backup and Restore
 Backup the entire local database and then restore it.
 The answer key
1. Backup the database:
Menu|Database|Database Backup > in the Choose a Backup Directory
dialog box, select a desired drive (hard drive or a removable drive), and
click New Dir button to create a new directory for the database backup >
click OK > the entire database is now backed up.
2. Restore the database from a backup:
Menu|Database|Database Restore > in the Choose a Backup Directory
dialog box, navigate to locate the backup directory, click OK > click Ok to
overwrite all current database files > click Ok to the “Are You Sure?”
question > click Yes to replace the existing address book > the entire
database is now restored.