Advanced Workshops on Vector NTI

1
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
2
Overview of the Workshop

• Navigate the Vector NTI Database Explorer
• Menu and Toolbar Comments
• Create New Database Subsets
• Edit or add new user-fields to database objects
• Search and report database objects
• Backup and archive databases
• Import, export, migrate databases
• Hands on Exercises

3
The Vector NTI Database Explorer
4
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 NTIs 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.

5
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 gt View gt OR Right click on mouse gt
  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 gt Arrange OR right click on mouse gt
  Arrange Icons

6
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 gt Right
click on mouse gt Columns gt Open the Options
dialog window gt customize the column selections
and layout. ?OR MenuView gt Options gt Details
View Tab Note The Options dialog window also
allows configuration of default settings for a
few other commands.
7
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)

8
Creating A New Database Subset

• Select Table gt New gt 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.
• Select Table gt New gt Subset (using Subset Editor)
  to create a new subset and select its contents in
  the Edit Subset dialog window.
• To create a new subset and place objects in it at
  the same time
• gt Select objects for the new subset in the
  Database Objects Pane gt click the New Subset
  button gt use the default name or enter a new
  name.

9
Adding or Removing Objects from A Database Subset

• The simple way of adding ? Open the source subset
  in the Subset Pane gt Select and drag selected
  objects from the list to the new subset.
• Add or remove objects from a subset
• Select the subset gt MenuTable gt Edit Subset gt
  Make selections in the Editing Subset dialog
  window.

10
Editing A Database Subset

• Dismiss a subset
• Select the subset gt MenuTable gt 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 gt MenuTable gt Table gt 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 gt MenuTable gt 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 gt MenuTable gt 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 gt then choose desire actions from the
  menu.

11
Editing a Subset Based on the Existing Subsets

• In the Subset Pane, select the subset gt
  MenuTableEdit Subset gt In the Editing subset
  dialog box, select all desired source subsets in
  the Source Subsets column gt Configure criteria
  (Intersection, Difference, Union) for the desired
  Source Content gt Select the desired molecules in
  the Source Content column gt Click Add button to
  add desired molecules to the Resulting Content
  column, which represents the subset being edited.
  gt 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.

12
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 gt
  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 gt Select MenuTable gt
  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 NTIs oligo
• text format (oligonucleotides).

13
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 gt 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.)
14
Export a Subset

• Export subset into a Vector NTI Archive
• Select MenuTable gt Export gt Subset into Archive
  to export all objects of the specified subset to
  a VNTI archive gt In the Write To dialog box,
  indicate the directory or folder, and file name
  for archive storage gt Click the Save button.
• Export All subset objects into a directory of
  text files (molecules and oligos only)
• Select MenuTable gt Export gt 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 NTIs oligo text format
  (oligonucleotides) gt In the dialog box, browse
  for the location and enter the file name under
  which the subset is to be stored.

15
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.

16
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 MenuDatabase gt Search OR
  Click the Search button gt in the Database Search
  Dialog Box, check the boxes for desired filters.

17
Basic Steps for Database SearchContinued
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 gt Click Start Search button.
5. Save the search results when the search
is finished, the Insert Search Results into
Subset dialog box will appear gt 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.
18
Configure the Database Search Filters the
Attribute Filters for DNA/RNA/Protein Molecules
19
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 gt check Author field gt type
yibu in New substring field gt Click Add
button gt Ok button Start Search gt save the search
results in a new subset yibu.
20
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 users last name, organism
  name, gene name, project name, etc.

21
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.

22
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 gt 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.

23
Configure the Database Search Filters the
Features Filter

• The Features Filter allows user to find molecules
  with specific features.
• Click the ltAdd button gt in the subsequent dialog
  box, select desired feature type and then one or
  multiple features within the group gt Click the OK
  button to complete the filter setup.
• Feature types differ for DNA/RNA searches and
  protein searches.

24
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.
25
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.
26
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.
27
Configure the Citation Database Search
The Citation Database Search allows users to
search citations by Citation, Text, and/or
Keywords.
28
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 gt
  Select desired reference gt MenuCitationCopy Tag
  gt 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 gt
  MenuCitationFormat Manuscript gt in the Format
  manuscript dialog box, click Browse button to
  select the RTF document gt in the Format reference
  for drop down menu, select a desired journal name
  gt Click Start button gt the tagged the document
  will be formatted with proper citations and
  bibliographies.

29
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
  gt Select desired references with Ctrl left
  mouse click
• 2. Generate the references In Citation Table gt
  MenuCitationCopy Bibliography gt In the Copy
  Bibliography dialog box, select the journal whose
  formatting the bibliography should follow gt click
  OK button.
• 3. Save the references Open your word
  processing document and paste the formatted
  citations.

30
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. MenuDatabase gt Database Backup gt 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. MenuDatabase gt Database
Restore gt in the Choose Backup Directory dialog
box, select the directory where the last backup
was stored gt 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.
MenuDatabase gt Database Cleanup.
31
Vector NTI Database Migration Strategies

• 1. Moving/copying entire database from PC to PC
• From Version 9.0 or later to Version 10
• gt Copy the entire database folder in the source
  PC (200-500 MB) gt Move the source folder to the
  hard drive of the target PC gt Open ONLY the
  Vector NTI Database Explorer on the target PC gt
  set the local database by MenuDatabaseSelect
  local database gt navigate to locate the database
  folder gt 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
• gt Archive each subset of each database table
  from the source computer gt 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.

32
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
• Select the DNA/RNA Molecule Table gt Sort the name
  column to locate CREB1 molecule gt click right
  mouse button gt Edit.
• In the Edit CREB1 dialog box gt browse all the
  tabs gt under the keywords tab, enter your last
  name and click Add. Note the Author change for
  CREB1.
• Click right mouse button on CREB1 gt
  ReportGeneral gt In Select Report Type dialog
  box, select New Report gt In Molecular Display
  Setup dialog box, select Default gt Browse the
  options in the Set General Report Options gt
  Browse the feature options in the Set Feature Map
  Options dialog box gt Click Finish button gt Print
  the report, or Click Camera button gt in the
  Camera dialog box, make desired selection and
  copy-to destination. The contents can be pasted
  to a word processor.

33
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
• Select the Protein Molecule Table gt Click on the
  Search Database Button.
• Configure the search criteria Check the Text
  Filter gt Set up the search for kinase in the
  Description Field gt Check the Attribute Filter gt
  Check the size 500 aa -1500 aa gt Click Start
  Search Button
• Save the search results to a new subset In the
  Insert search results into subset dialog box,
  enter the new subset name gt Click Ok button.

34
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
• Select the Protein Molecule Table gt Click on the
  Search Database Button.
• Configure the search criteria Check the Feature
  Filter gt Click Add gt In the Add Features dialog
  Window, locate the Transmembrane feature under
  the Protein Functional Features gt Domainsgt Check
  Add all features of this type gt Click OK gt Click
  OK gt Click Start Search
• Save the search results to a new subset In the
  Insert search results into subset dialog box,
  enter the new subset name gt Click Ok.

35
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 gt
  MenuTableExportSubset into a directory of text
  file gt in Export Protein To dialog box, create a
  new folder on the desktop and enter the subset
  name as the file name, click OK gt all molecules
  in the new subset are now exported into the
  directory.
• 2. Archive a Subset
• Select the newly created subset gt
  MenuTableExportSubset into Archive gt 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 gt a single
  archive file is created.
• 3. Delete the newly created subset gt Select
  the subset in the Subset Pane gt TableDelete
  Contents from Database gt TableDismiss Subset

36
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,
  MenuTableProtein Molecules gt MenuTableImportM
  olecules from Directory of Text Files gt in the
  Import Proteins dialog box, locate the folder,
  and select the protein list file (.pls file) gt
  click Open gt in the Insert Protein Molecules into
  Subset dialog box, enter the name for the new
  subset gt 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,
  MenuTableProtein Molecules gt MenuTableImportM
  olecules from Archive gt in the Import Protein
  Archive From dialog box, locate the protein
  archive file (.pa4 file), click Open gt in the
  Insert Protein Molecules into Subset dialog box,
  enter the name for the new subset gt click OK, and
  all the molecules in the archive file are
  successfully imported into the new subset.

37
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
• MenuDatabaseDatabase Backup gt 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 gt click OK gt the entire
  database is now backed up.
• 2. Restore the database from a backup
• MenuDatabaseDatabase Restore gt in the Choose a
  Backup Directory dialog box, navigate to locate
  the backup directory, click OK gt click Ok to
  overwrite all current database files gt click Ok
  to the Are You Sure? question gt click Yes to
  replace the existing address book gt the entire
  database is now restored.