Vector NTI database contains DNA/RNA molecules, protein molecules, enzymes (restriction endonucleases), oligonucleotides (including PCR primers, sequencing primers and hybridization probes), and gel markers. These objects are held in separate database tables – one table per object type. The database tables also contain a list of named subbases (subsets) of objects to help you organize your work. You can edit the contents of subbases, take their intersections, differences, and unions, and use them to work with organized groups of database objects.

Vector NTI Subbases

A subbase is a subset of objects in a certain table of the Vector NTI database. Use subbases to organize database objects (molecules, enzymes,...) you create into categories. You might have one subbase for each of your molecule families, one for each taxonomic group, etc.

Each database object can be included in any number of subbases. Adding a database object to a subbase does not increase the amount of disk storage the object occupies.

Subbases are created, edited and deleted through the Database Explorer.

There are several system subbases which may appear and disappear during Vector NTI work and cannot be modified by the user:

The MAIN subbase contains all database objects in a given table.

The <MOLNAME>_$Construction Options subbase in the DNA/RNA Molecules table contains the construction options created during the last construction of molecule <MOLNAME>.

The <MOLNAME>_$Design Options subbase in the DNA/RNA Molecules table contains the design options created during the last creation of molecule <MOLNAME> with the aid of Vector NTI's built-in biological knowledge.

The <MOLNAME>_$Intermediate subbase in the DNA/RNA Molecules table contains the intermediate molecules created during the last creation of molecule <MOLNAME> with the aid of Vector NTI's built-in biological knowledge.

Database object fields

Each database object is described by a set of fields, describing various parts of object data. Each object type defines its own set of fields; some of these fields are common for all database objects, others are specific for a particular object type. The fields from the standard set are called system fields. A user may also define additional User Fields to extend Vector NTI database model.

Vector NTI assigns names to most of object fields and makes them accessible in a uniform manner from various parts of the program’s user interface. Not all system fields are accessible in this way; some of them, for example molecule feature table, are only visible in specialized object type–specific dialogs or Display windows.

Vector NTI has mechanisms for tracking authors, original authors, and times of creation and modification for all database objects. The information is stored in the following named system fields which are the same for all database objects:

Original Author - name of Vector NTI user who created the object,
Author - name of Vector NTI user who last modified the object,
Creation Date - date and time when the object was created,
Modification Date - date and time when the object was last modified in the local Vector NTI database.

When you start Vector NTI for the first time, it displays the Author Information dialog allowing you to identify yourself as Vector NTI user and author of all modifications and new objects you create in the local database. By default, it presents the name given to the Vector NTI Installation program. You can change the name and supply additional contact information about yourself in this dialog. The information you provided will be automatically attached to all database objects you created and/or modified when you export them, copy to shared databases etc. Although you can call up this dialog any time later using the Author Info command from the File menu of the main Vector NTI window and change some or all information in this dialog, we would not recommend it because these later changes do not affect information stored in database objects you submitted to shared databases earlier.

When you create an object in your database, this object is marked as a "Local Object" and you become both the author and the original author of it. For local objects the information about the authors is often not displayed while you are viewing or editing the objects because of its obvious redundancy. When you then export the object into an external file or Vector NTI archive, or transfer it to a Vector NTI Shared Database , the object "remembers" its authors and this information is displayed when another Vector NTI user views the object.

When you import an object from an external file or Vector NTI archive, or transfer it from a Vector NTI Shared Database into your local database, the program checks the object's author. If you are the author, the object will still be marked as "Local", but if the author is someone else, then the object is marked as "Foreign" and the information about its authors is always displayed when you are viewing or editing the object.

The original author (creator) of an object, either "Local" or "Foreign", never changes. But if you modify a "Foreign" object, it'll become "Local" and you'll become its new "immediate" author.

If you are importing an object in which author or original author information is not stored in your contact database, the program will recognize this and ask whether you want to automatically add the appropriate contact records to the contact database. It also will ask whether you want to automatically update the record if the author data in the imported object differ from the contact record stored in your contact database under the same person's name.

You can change the date/time display format using the Options command from the Edit menu of the main Vector NTI’s window. The General page of the Options dialog box allows you to choose between the standard US date format (i.e. 03/20/96 04:20PM) and a regional date/time format. The regional format is the default Windows format; you can change this format using the Windows Control Panel / Regional (or International) dialog.

Authors, original authors, and times of creation and modification for all database objects are updated automatically by Vector NTI and should not, in normal circumstances be modified manually. But if such a need occurs, you have a Set System Attributes command for setting values of these fields in the Vector NTI Database Explorer (see below).

Here is the full list of named system fields displayed by Vector NTI:

Field name	Description	Used in: N(DNA/RNAs) P(proteins) E(enzymes) O(oligos) G(gel markers) C(contacts) U(user field defs)
Name	Name of an object	NPEOGCU
Local/Foreign	Object’s ‘ownership’ status in the local database	NPEOG (local DB only)
Original Author	Original author (creator) of an object	NPEOG
Created	Date of an object’s creation	NPEOG
Author	Author of the last modification to an object	NPEOG
Modified	Date of the last modification to an object	NPEOG
Submitted by	The name of a Vector NTI user who submitted the object	NPEOG (shared DB only)
Description	Description string	NPEOGU
Form	Circular or Linear	N
Storage Type	Basic, Designed or Constructed	NP
Fully Processed?	Molecule’s construction status	N
Length	Length of a molecule/oligo/enzyme’s recognition string in bp	NPOE
DNA/RNA	nucleic acid type	NO
Degenerate?	Is an oligo degenerate?	O
Oligo Sequence	Oligo’s nucleotide sequence	O
Recognition String	Enzyme’s recognition string	E
Terminus Type	Enzyme’s terminus type	E
Palindromic?	Is an enzyme palindromic?	E
Ambiguous?	Is an enzyme ambiguous?	E
Number of Fragments	Number of fragments in a gel marker	G
Longest Fragment	Length of the longest fragment in a gel marker	G
Shortest Fragment	Length of the shortest fragment in a gel marker	G
Telephone	Phone part of the Contact info	C
E-mail	E-mail part of the Contact info	C
Field Type	User field type	U
Indexed?	Is user field cached/indexed?	U
Default	Default value of a user field	U
List of Predefined Values	List of predefined values of a user field	U
Record #	Database record ID number	NPEOG

In addition to the named system fields above, every database object has comments and keywords associated with it. These fields are accessible from within specialized object editors and Display windows.

Note All automatically updated fields, user-defined fields and comments are searchable. Using the database search interface described in this chapter you can perform string context searches through any of the fields above for any database objects.

User-defined Fields

Many researchers use Vector NTI as a major tool for storing and managing their laboratory experiment-related information. In order to generalize the Vector NTI database and make it suitable for a wider range of information management functions, Vector NTI allows you to associate User Fields with any database object (molecules, oligos, etc.). A User Field may contain any laboratory-specific and user-specific information necessary for an appropriate description of the object. User Fields can be imported, exported, displayed, printed and managed just as the regular database fields.

Vector NTI maintains a local list of descriptions of "known" User Fields that are presented to the user when he or she creates new database objects. The objects you import from other Vector NTI databases can contain fields that are not described in the local list. Vector NTI always stores all imported User Field information in the database (so no information is lost) and allows you to view it. However, if some of the object’s fields are not described in the local User Field Definition list, Vector NTI will ask and help you to add their descriptions to the list whenever you try to edit the information contained in these fields. To simplify the process of maintaining the same list of User Field Definitions across several Vector NTI Databases, Vector NTI allows you to import and export User Field Definitions.

The "User Fields Manager" section of this chapter contains the detailed description of all User Fields-related operations.

Comments

In addition to the description string and user-defined fields, each database object can contain a text comment of unlimited length. Vector NTI automatically converts stored comments when importing or exporting molecules from/to GenBank/GenPept and EMBL/SWISS-PROT files.

Comments may be edited in the Comments pages of the objects' editors or immediately in the Molecule Display window (for molecules only). When you open a Display window for a database molecule, the Text pane of the window has the Comment line and icon. Double clicking on this line or clicking on the icon calls up the Comment Editor containing the molecule comment (if any).

Keywords

Each database object can contain a list of associated keywords. Keywords may be edited in the Keywords pages of the objects' editors. Keywords are very useful for database searches.

Vector NTI archives

Vector NTI allows you to place your DNA/RNA and protein molecules, enzymes, oligonucleotides, and gel markers into "archives"—data files of special format—which may be transferred to another computer (Mac or PC) and read by Vector NTI running on that computer. So, the archives give you the possibility to share you objects (for instance, your own molecule constructs) with your colleagues, or to have them simultaneously on several computers (for instance, at work and at home).

There are two important points with Vector NTI archives. The first is that all the DNA/RNA molecule information will be written to and read from archive including molecule component fragments (if the molecule is constructed from other molecules) and parent-descendant connections between molecules. The second is that Vector NTI automatically checks the consistency of molecule archive. Imagine that you place a number of your constructs into an archive to give them to your colleague but forget to include some of the parents of those constructs. Your colleague may have problems dealing with them: if she, for instance, wants to reconstruct some of your molecules, the program will not find necessary parents in his database. But Vector NTI will check this and many other situations on the stage of archive creation and allow you to solve the problem, automatically adding necessary parents (including DNA parents of translated protein molecules) or disconnecting them. Also when the archive is loaded into new database, Vector NTI will check if it affects any of database molecules and recalculates them if necessary.

Vector NTI Database Explorer

Vector NTI 4.0 Deluxe introduced the Vector NTI Database Explorer: a user interface component allowing easy management of the Vector NTI database contents. Vector NTI Explorer is integrated into the Windows 95/98/Windows NT shell interface. The following description of Vector NTI Explorer assumes that you are familiar with the Windows 95//98/NT Explorer (we will use the words "the Explorer" to refer to Vector NTI Explorer, not to Windows Explorer). The user interface of the two Explorers is very similar; you can browse local and shared Vector NTI databases in the same intuitive manner you browse your files. For example, Vector NTI Explorer allows you to rename database objects by typing a new name directly in the Explorer window; it supports clipboard data exchange as well as drag and drop operations between Vector NTI databases and file system.

The Vector NTI Explorer windows display the contents of the local and shared databases. Since there is only one local database and at most one shared database you can connect to at a time, you will not see more than two Vector NTI Explorer windows simultaneously. Vector NTI databases (both local and shared) consist of several tables: the Molecule Table, the Enzyme table etc. Each table contains zero or more database objects or items of the appropriate type. The Explorer window displays the contents of one table at a time. You may switch between tables by selecting a table from the Table menu or Table combo box in the top left corner of the Explorer window. Each window has two panes, one for subbases (named subsets of database objects), another for objects themselves.

When you select a subbase in the left pane, the Explorer displays its contents in the right pane. You may select one or more database objects and perform various operations on them. The Explorer uses menus to show available database operations. The first menu in the Explorer’s menu bar is context-sensitive—it displays table- and subbase-related commands when the subbase pane is active and object-related commands when the object pane is active. To switch between panes you can click with the mouse on a pane you want to activate or use the F6 or TAB keyboard shortcuts. You can also access the context-sensitive menus by clicking on subbases or database objects with the right button. The Explorer displays a shortcut menu containing commands appropriate for the object under the cursor.

Database Search

Vector NTI has powerful database search capabilities. To perform a database search, press the Search button in the Database Explorer toolbar or choose the Search command from the Explorer’s Database menu. Depending on the object type the appropriate Database Search dialog box appears allowing you to define search filters and perform the actual search (see detailed descriptions of filters below). When you are satisfied with the search setup, press the Start Search button. If Vector NTI finds any objects by a database search, the appropriate Subbase Name dialog box appears. Enter a name of subbase or choose a name from the list of existing subbases. All objects found will be placed in the specified subbase overwriting the existing subbase content (if any).

Note If the specified subbase already exists, Vector NTI empties it before adding found objects. You can refine your search by using the resulting subbase to limit the search space of the next search.

DNA/RNA Molecule database search

In the DNA/RNA Database Search dialog box you can specify a subbase to search and setup one or more filters allowing you to find only those molecules that satisfy all the conditions you chose.

Attributes Filter

Check the Attributes Filter box to filter search results based on various molecule attributes. The attributes used by the filter can be set by pressing the Attributes Setup button. The Conditions dialog will appear, consisting of groups of related attributes.

To set search conditions in any of the group boxes, check conditions describing the molecules you want to find. A molecule will be accepted by the search if it satisfies at least one of the conditions checked in each group.

If all conditions in a group are checked, or all conditions in a group are blank, that group has no effect on the search.

Text Filter

Check the Text Filter box to filter search results based on text inside various object fields. The filter can be set up by pressing the Text Setup button.

The Conditions dialog will appear, allowing you to define one or more substrings that should be present in the text of one or more of the specified object fields. You may also choose between case-sensitive and case-insensitive search options.

Keywords Filter

Check the Keywords Filter box to filter search results based on keywords associated with an object. The filter can be set up by pressing the Text Setup button. The Conditions dialog will appear, allowing you to choose the keywords to search for.

Molecules that have any one of the keywords shown in this box will be found by the search. Press the Add button to select from the list of existing keywords. To remove a keyword from the box after it has been added, select it and press the Remove button. To clear the Keywords box, press the Remove All button.

Ancestors Filter

Check the Ancestors Filter box to filter search results based on immediate molecule ancestors. The filter can be set up by pressing the Ancestors Setup button. The Conditions dialog will appear, allowing you to chose one or more DNA molecules.

Molecules that have as a direct ancestor any one of the molecules shown in this dialog will be found by the search. To add a molecule to this box, press the Add button. A dialog box appears, allowing you to choose from the molecules in the database. Select the molecules you need, and choose OK. To remove a molecule from the list, select the molecule and press Remove. To clear the Direct Ancestors list, press the Remove All button.

Oligo & Peptides Filter

Check the Oligo & Peptides Filter box to filter search results based on homology between target molecules and given oligonucleotides and short peptides. The filter can be set up by pressing the Oligo & Peptides Setup button. The Conditions dialog will appear, allowing you to chose oligonucleotide and peptides for homology search.

To add an oligonucleotide for homology search, press the Oligo button. To add a peptide for homology search, press the Peptide button.

To remove a search condition from the Oligonucleotides/Peptides list box, select the condition and press the Delete button. To clear the Oligonucleotides/Peptides box, press the Clear button.

Features Filter

Check the Features Filter box to filter search results based on presence of certain features. The filter can be set up by pressing the Feature Setup button. The Conditions dialog will appear, allowing you to chose feature types and feature names for feature search.

To add a feature to the search conditions, press the Add button. A dialog box appears, allowing you to define restrictions on the molecule’s feature map.

Select a feature type from the feature classification tree and, optionally, one or more feature names. You can add a condition consisting of a feature type without specific feature names. If you define a type of feature but no specific feature names, the search condition will be defined as any feature of that type. The defined condition appears in the Feature list in the conditions dialog.

To remove a search condition from the Features list, select the condition and press the Remove button. To clear the Features list, press the Remove All button.

Protein database search

In the Protein Database Search dialog box you can specify a subbase to search and setup one or more filters allowing you to find only those proteins that satisfy all the conditions you chose

Protein molecules search filters are the same as ones for DNA/RNA molecules search described above. The only exception is Oligo & Peptides Filter that allows you to specify only peptides (the Oligo button in the Conditions dialog is disabled).

Enzyme database search

In the Enzyme Database Search dialog box you can specify a subbase to search and setup one or more filters allowing you to find only those enzymes that satisfy all the conditions you chose.

Recognition String Filter

The Recognition String filter allows you to enter a nucleotide string which must be found in the recognition site of the desired enzyme.

Attributes Filter

Use the Attributes Filter box to filter search results based on various enzyme attributes. An enzyme will be accepted by the search if it satisfies at least one of the checked conditions. You can restrict the length of the recognition site, specify whether it can be ambiguous or non-ambiguous, and whether it can be palindrome or non-palindrome. "Ambiguous" recognition site means the site containing any nucleotide besides A, T, G, or C.

Text Filter

Check the Text Filter box to filter search results based on text inside various object fields. The filter can be set up by pressing the Text Search Setup button. The Conditions dialog will appear, allowing you to define one or more substrings that should be present in the text of one or more of the specified object fields. You may also choose between case-sensitive and case-insensitive search options.

Keywords Filter

The Keywords Filter allows you to filter search results based on keywords associated with an object. Only enzymes that have any one of the keywords shown in the Keywords list box will be found by the search. Press the Add button to select from the list of existing keywords. To remove a keyword from the box after it has been added, select it and press the Remove button. To clear the Keywords box, press the Remove All button.

Oligo database search

In the Oligo Database Search dialog box you can specify a subbase to search and setup one or more filters allowing you to find only those oligos that satisfy all the conditions you chose.

Nucleotide String Filter

The Nucleotide String filter allows you to enter a nucleotide string which must be found in the sequence of the desired enzyme.

Attributes Filter

Use this filter to limit search space to DNAs only or RNAs only. If both check boxes are checked or unchecked, the filter has no effect.

Text Filter

Keywords Filter

The Keywords Filter allows you to filter search results based on keywords associated with an object. Only oligos that have any one of the keywords shown in the Keywords list box will be found by the search. Press the Add button to select from the list of existing keywords. To remove a keyword from the box after it has been added, select it and press the Remove button. To clear the Keywords box, press the Remove All button.

Gel marker database search

In the Gel Marker Database Search dialog box you can specify a subbase to search and setup one or more filters allowing you to find only those gel markers that satisfy all the conditions you chose.

Attributes Filter

Use this filter to limit search space to gel markers with specified length of the longest fragment. If all check boxes are checked or unchecked, the filter has no effect.

Text Filter

Keywords Filter

The Keywords Filter allows you to filter search results based on keywords associated with an object. Only gel markers that have any one of the keywords shown in the Keywords list box will be found by the search. Press the Add button to select from the list of existing keywords. To remove a keyword from the box after it has been added, select it and press the Remove button. To clear the Keywords box, press the Remove All button.

Database Operations

Backup, Restore and Cleanup

There are three general functions dealing with the entire database: Database Backup, Database Restore, and Database Cleanup.

The Database Backup function makes a copy of your database in a specified directory or folder. For instance, you may backing up the data to removable storage to make a permanent, safe record of your database. Making such a backup is the only way to be sure your data is safe in the case of hard drive failure.

The Database Restore function restores all database files from the last backup. Your database is restored from a specified directory or folder, overwriting all current database files.

The Database Cleanup function allows you to remove all the "garbage" data from the data files and database tables. These data may be accumulated when you extensively create and delete database objects. Although these data do not affect Vector NTI functionality, we recommend you to make database cleanup once a week.

All three general database functions are available from the Database menu of the Database Explorer.

Operations on Subbases

Vector NTI Database Explorer allows you to perform common operations on groups of database objects arranged into subbases (named subsets). Subbases are listed in the left pane of the Explorer; to invoke a command associated with a subbase one need to click on its name in the left pane and use the Table menu. Most of the subbase commands are also accessible from the shortcut menu associated with a subbase.

New 4 Subbase
New 4 Subbase for Selection

Use these operations to create a new subbase containing selected objects (if any). The Explorer creates a new subbase with a default name and allows you to edit this name. This operation does not affect database objects.

New 4 Subbase (Using Subbase Editor)

Use this operation to create a new empty subbase and call the Subbase Editor to define its contents. The Subbase Editor is described below.

Edit Subbase

Use this operation to edit the selected subbase. It is not available for subbases in which the content is maintained automatically.

This operation brings up the Edit Subbase dialog box:

This dialog box has three columns. The Source Subbases column shows all of the subbases in your Vector NTI database table except the one you are editing. The Source Content column shows logical combinations of objects present in the subbases which are highlighted in the Source Subbases column. The Resulting Content column shows the contents of the subbase you are editing.

Adding objects to a subbase

To add objects to the subbase you are editing, highlight one or more subbases in the Source Subbases column.

When one or more source subbases are highlighted, the Source Content column of the dialog box shows a logical combination of the objects in those subbases.

If the Intersection radio button under the Source Subbases column is selected, the Source Content column shows the logical intersection of the subbases highlighted in the Source Subbases column, i.e. only those objects present in all highlighted subbases.

If the Difference radio button under the Source Subbases column is selected, the Source Content column shows the logical symmetrical difference of the subbases highlighted in the Source Subbases column, i.e. each object present in exactly one of the highlighted subbases.

If the Union radio button under the Source Subbases column is selected, the Source Content column shows the logical union of the subbases highlighted in the Source Subbases column, i.e. each object present in at least one highlighted subbase.

If only one subbase is highlighted, the Intersection, Difference, and Union buttons are deactivated, and all the objects in that subbase are shown in the Source Content column.

To include objects in the subbase you are editing, highlight their names in the Source Content column. You can use the Select All and Unselect All buttons below the Source Content column to highlight or deselect all objects at once. When the objects you want are highlighted, press the Add button to add them to the Resulting Content column.

Removing molecules from a subbase .

The Resulting Content column shows the current contents of the subbase you are editing. To remove objects from the subbase, highlight their names in the Resulting Content column and press the Remove button. Select All and Unselect All buttons below the Resulting Content column allow you to highlight or deselect all objects in the column.

When you are done editing a subbase.

When you are finished editing a subbase, choose OK to exit the Editing Subbase dialog box. The contents of the Resulting Content column will be recorded as a new contents of the edited subbase.

Subbase editing does not affect database objects.

Rename Subbase

Use this operation to rename the selected subbase. The Explorer displays a small edit box where you can change the name of the subbase.

This operation does not affect the subbase contents and database objects.

This operation is not available for subbases in which the content is maintained automatically.

Dismiss Subbase

Use this operation to exclude all objects from the selected subbase and remove the subbase itself. To empty a subbase, use the Clear Subbase operation.

This operation does not affect the database objects; they are still stored in the database and included in all other subbases where they were included before this operation.

Clear Subbase

Use this operation to exclude all objects from the selected subbase. The subbase itself will be emptied but not removed. To remove a subbase, use the Dismiss Subbase operation.

This operation does not affect the database objects; they are still stored in the database and included in all other subbases where they were included before this operation.

This operation is not available for subbases in which the content is maintained automatically.

Delete Contents

Use this operation to physically delete from the database all objects of the specified subbase. Vector NTI asks you to confirm that you want to physically delete the objects listed in that subbase. If you choose OK, the objects in the subbase are permanently deleted from the Vector NTI database, and the subbase itself is removed.

Deleting all objects in a subbase is particularly useful in case of molecules if you have created many molecules with the help of Vector NTI’s built-in biological knowledge, leaving many intermediate recombinants taking up extra storage space.

Subbase Summary

Use this operation to create a text file containing a summary of the specified subbase. A standard File Save dialog appears. Indicate the directory or folder, and file name in which you would like to store the summary. Press the OK button (Windows) or Save button (Macintosh), and Vector NTI creates the summary.

Subbase Properties

This operation displays the selected subbase information.

Import From Vector NTI Archive

Use this operation to import objects from a Vector NTI archive. A standard File Open dialog will appear. Indicate the directory or folder, and archive file you would like to read from. Press the OK button (Windows) or Open button (Macintosh), and Vector NTI performs the import.

Note You can also read the Vector NTI archives from the Vector NTI File menu. Select the Import...Molecules/Enzymes/Oligos/Gel Markers From Archive command from the File menu. The procedure is exactly the same as in case of import from Database Explorer.

Export Into Vector NTI Archive

Use this operation to export all objects of the specified subbase to a Vector NTI archive. A standard File Save dialog appears. Indicate the directory or folder, and file name in which you would like to store the archive. Press the OK button (Windows) or Save button (Macintosh), and Vector NTI creates the archive.

Import Objects From Directory of Text Files XE " (molecules and oligos only)

Use this operation to import molecules and oligonucleotides from a directory of text files. The files must be in the GenBank format (DNA/RNA molecules), GenPept format (protein molecules) or Vector NTI's oligo text format (oligonucleotides). You will be asked for the List File describing the objects you are going to import. When Vector NTI exports the objects into a directory of text files (see below) it automatically creates the appropriate List File.

Export All Subbase Objects Into Directory of Text Files (molecules and oligos only) )

Use this operation to export all objects of the specified subbase into a directory of text files. The files will be in GenBank (DNA/RNA molecules), GenPept (protein molecules) or Vector NTI's oligo text format (oligonucleotides). You will be asked for a name of the List File which Vector NTI will create to describe the objects you are importing.

Import Molecule From Text File XE "

Use this operation to import DNA/RNA or protein molecule data from a GenBank/GenPept, EMBL/SWISS-PROT, or FASTA file. Vector NTI imports all molecule data including feature table (if any).

The Import Molecule dialog box will appear allowing you to choose the appropriate import file format—GenBank, EMBL, or FASTA for DNA/RNA molecules and GenPept, SWISS-PROT or FASTA for proteins. Press the OK button and the standard File Open dialog will appear. Indicate the directory or folder, and file you would like to import. Press the OK button (Windows) or Open button (Macintosh), and Vector NTI reads the file, checks all data, creates the new molecule, and shows you new molecule’s data in the Molecule Editor dialog box. After entering or editing new molecule’s data, press the OK button and Vector NTI saves the new molecule into the database.

Import Sequence From Text File

Use this operation to import the nucleotide or amino acid sequence from a text file and create a new DNA/RNA or protein molecule containing this sequence. The standard File Open dialog will appear. Indicate the directory or folder, and file you would like to import. Press the OK button (Windows) or Open button (Macintosh), and Vector NTI reads the file, checks all data, creates the new molecule, and shows you new molecule’s general data in the Molecule Editor dialog box. After entering or editing the new molecule’s data, press the OK button and Vector NTI saves the new molecule into the database.

Format for ASCII sequence files

An ASCII sequence file must obey the following rules:

1. It must be a plain (ASCII) text file (not a file in WordPerfect, or MS Word formats).

2. The file must contain the nucleotide (amino acid) sequence arranged in lines. Each line may contain the following:

1.Nucleotide (amino acid) symbols and whitespace, or

2.A number followed by whitespace and nucleotide (amino acid) symbols (i.e., similar to GenBank format), in which case the number will be ignored, or

3.A number only, in which case the number will be interpreted as a block of unknown nucleotides (amino acids) of the corresponding length.

The following characters are used to represent nucleotides throughout Vector NTI:

a

adenine

t

thymine

c

cytosine

g

guanine

r

purine (A or G)

y

pyrimidine (C or T)

w

a or t

s

c or g

m

a or c

k

t or g

b

c, g, or t

d

t, g, or a

h

c, a, or t

v

c, g, or a

n

unknown nucleotide

Amino acids are represented by standard 1-letter codes:

A

Alanine

R

Arginine

N

Asparagine

D

Aspartic acid

C

Cysteine

Q

Glutamine

E

Glutamic acid

G

Glycine

H

Histidine

I

Isoleucine

L

Leucine

K

Lysine

M

Methionine

F

Phenylalanine

P

Proline

S

Serine

T

Threonine

W

Tryptophan

Y

Tyrosine

V

Valine

X

unknown amino acid

*

stop codon (not an acid)

Note You can also import molecules and sequences from the Vector NTI workspace’s File menu. Select the Import4 (DNA/RNA or Protein) Molecule From Text File or Import4 (Nucleotide or Amino Acid) Sequence From Text File command from the File menu. The procedure is exactly the same as in case of import from Database Explorer.

Note GenBank, GenPept and EMBL feature tables usually do not contain names for features. When importing, Vector NTI will assign "artificial" names for the features so that they will be recognizable on a graphics map. You can change features’ names after import using Vector NTI’s Molecule Editor, or assign names to features before import, by adding "label=<name>" descriptors in the flatfile for any desired features. Here is a sample GenBank/EMBL feature description with a defined feature name:

CDS 86..1276

/label=TC(R)

For more information about GenBank/GenPept /EMBL Feature Table descriptors, see the GenBank/GenPept /EMBL documentation.

Import Enzymes From REBASE Database

Vector NTI allows you to import restriction endonucleases from the widely known REBASE database which is available through Internet from the anonymous FTP site vent.neb.com (directory pub/rebase). For recent review of REBASE database see Nucleic Acids Research 22: 3628-3639, 1994.

Each REBASE release contains several data files in different formats. Vector NTI uses Bairoch format, so you have to download the bairoch.### file where ### indicates the current version (e.g., 506 indicates June 1995). Distributive version of Vector NTI contains the last release of the REBASE bairoch.### file in the Vector NTI working directory.

To import restriction endonucleases from REBASE database, use the Import Enzymes From REBASE Database command. A standard File Open dialog will appear. Indicate the directory or folder, and choose the bairoch.### file you would like to import. Press the OK button (Windows) or the Open button (Macintosh), and Vector NTI reads the file, checks all data, and loads REBASE enzymes to the REBASE Enzymes dialog box:

You can filter the enzymes in the Source Enzymes / Selected columns. To do that, check on or off the appropriate boxes in the Use REBASE Subset group in the lower right corner of the dialog box and press the Hide Others button.

When all the desired enzymes are in the Selected list, press Import Selected button to import them into Vector NTI.

Import New Enzymes From REBASE Database

The same as the previous REBASE Import command but allows you to import only those enzymes which are currently not in the Vector NTI database.

Operations on Database Objects

To perform various operations on individual database object or group of one or more objects, you can select the objects in the right pane of the Database Explorer and invoke commands from the leftmost menu named after the type of the currently displayed table. Most of the object-related commands are also available from the objects’ shortcut menu.

Common operations

This section lists operations that are common for all types of database objects.

Open

Use Open to open Display windows for selected objects. This operation is available only for DNA/RNA and protein molecules.

Import…

Import operations are described in the previous section ("Operations on Subbases").

Export Selection into Archive

Use this operation to export selected objects to a Vector NTI archive. A standard File Save dialog appears. Indicate the directory or folder, and file name in which you would like to store the archive. Press the OK button (Windows) or Save button (Macintosh), and Vector NTI creates the archive.

Exclude from Subbase

Use this operation to exclude selected database objects from the current subbase. This operation does not affect the objects themselves; they are still stored in the database and included in all other subbases where they were included before this operation.

Delete from Database

Use this operation to physically delete a specified database object. Vector NTI asks for confirmation before deleting the object.

If a DNA molecule is deleted, Vector NTI scans all its descendants and disconnects them from the deleted molecule.

Rename

Use this operation to rename the selected object. The Explorer displays a small edit box where you can change the name of the object.

If a DNA molecule is renamed, Vector NTI scans all its descendants and also changes molecule’s name in all component fragment descriptions of all the molecule’s descendants.

Duplicate

Use this operation to make copies of the selected database objects. The replicas of selected objects will be created in the database and included into the current subbase. The replica of an object named ‘x’ will be called ‘Copy of x’. Note, that copies of objects are just snapshots of their current state; they are not related to original objects (i.e., a copy of a molecule is not a descendant of the original molecule). It logically follows then, that "copies" do not track further changes you may make to the originals.

Properties

This operation displays the properties of the selected object or objects. If exactly one object is selected, Vector NTI displays all the named object fields with their values. Some object data (like molecule sequence and comments) are not stored in named fields and are not displayed in the properties dialog. For molecules, the property dialog has two extra pages: Parents and Descendants. These pages display Parent and Descendant trees for the selected molecule.

Note This operation is also available for objects displayed in the Database Select Object/New Object dialogs (see below).

Set System Attributes

This operation allows you to manually modify the automatically updated fields of the selected objects - Author, Original Author and Creation Date. When you choose this command, Vector NTI calls up the Set System Attributes dialog box. The dialog box has three check boxes indicating if you would like to update the appropriate field. If a check box is set to On, the combo box (edit box in case of Creation Date) below the check box is activated allowing you to set the value of the appropriate field.

The Author and the Original Author fields may be set only with the names of contacts already stored in the contact database. The Creation Date field must be set with a date and time in the USA format: "MM/DD/YY H:MIN AM(or PM)" where H is from 1 to 12.

DNA/RNA molecule operations

This section lists operations that are applicable to DNA/RNA molecules only.

Edit

Use this operation to edit the selected DNA/RNA molecule. Vector NTI displays the Molecule Editor dialog and allows you to change the molecule. the Molecule Editor dialog box is described in Chapter 14 of the Manual. You may use the Open command to edit molecule in the Molecule Display window.

New Molecule Using Sequence Editor

Use this operation to create a new DNA/RNA molecule entering its nucleotide sequence by hand with the aid of Vector NTI Sequence Editor. The operation brings up the Molecule Editor dialog box described in Chapter 14 of the Manual.

New Molecule (Using Construct/Design Procedure)

Use this operation to create a new DNA/RNA molecule using the construction procedure or Vector NTI's built-in biological knowledge. The operation brings up the Construct/Design Molecule dialog box described in Chapter 14 of the Manual. The construction process is also described in Chapter 14. The design process is described in Chapter 16.

Export Molecule into Text file

Use this operation to export a selected molecule into a GenBank, EMBL, or FASTA file.

Export Sequence into Text file

Use this operation to export the nucleotide sequence of the selected molecule into a text file.

Re-Construct

Use this operation to re-construct a previously constructed DNA/RNA molecule. The operation brings up the Construct/Design Molecule dialog box filled with the specified molecule. The dialog box and the construction process are described in Chapter 14.

Re-Design

Use this operation to re-design a specified DNA/RNA molecule using Vector NTI’s built-in biological knowledge. The molecule must be previously designed by Vector NTI. The operation brings up the Construct/Design Molecule dialog box filled with the selected molecule. The Component Fragment section of the dialog box will contain the component fragments constituting the original design task for the molecule. The dialog box is described in Chapter 14. The design process is described in Chapter 16.

Change Starting Coordinate

Use this operation to change the starting coordinate of a selected molecule. This operation changes a molecule’s starting coordinate not only in the molecule’s data file but also in all component fragment descriptions of all the molecule’s descendants (if necessary).

Delete with Descendants from Database

Use this operation to physically delete the selected DNA molecule together with its descendants (DNA/RNA and protein molecules). Vector NTI asks for confirmation before deleting the molecules.

Protein molecule operations

This section lists operations that are applicable to protein molecules only.

Edit

Use this operation to edit the selected protein molecule. Vector NTI displays the Molecule Editor dialog and allows you to change the molecule. the Molecule Editor dialog box is described in Chapter 14 of the Manual. You may use the Open command to edit molecule in the Molecule Display window.

New Molecule Using Sequence Editor

Use this operation to create a new protein molecule entering its amino acid sequence by hand with the aid of Vector NTI Sequence Editor. The operation brings up the Molecule Editor dialog box described in Chapter 14 of the Manual.

Export Molecule into Text file

Use this operation to export a selected molecule into a GenPept, SWISS-PROT, or FASTA file.

Export Sequence into Text file

Use this operation to export the nucleotide sequence of the selected molecule into a text file.

Enzyme operations

This section lists operations that are applicable to RENs only.

Edit

Use this operation to edit the selected REN. Vector NTI displays the Enzyme Editor dialog described below. You need to use the Rename command to change the enzyme’s name.

New Enzyme

Use this operation to create a new database enzyme. The Enzyme Editor tabbed dialog appears:

You may enter information about the new REN as follows:

In the name box on the General Page, enter the name of the REN.
In the Recognition String box on the Enzyme page you may enter the enzyme’s recognition string.
In the Cleavage Point field on the Enzyme page, enter the number of the nucleotide immediately after the direct-strand cleavage point. The following figure demonstrates how cleavage points of palindromic sites are defined:

If the REN has a non-palindromic recognition site, the Cleavage Point on Complementary Strand field will be enabled. In this field, enter the number of the nucleotide immediately after the complementary-strand cleavage point.

The following figure demonstrates how cleavage points are defined for non-palindromic sites on both direct and complementary strands:

The preview box on the Enzyme page will help you to enter cleavage points.
In the Description box on the Enzyme page, enter the REN’s description.
Use the User Fields page to add custom data in a form of fields (User Fields section for details)
Use the Comments page to enter text comments.
Use the Keywords page to enter key words for the REN. To add a key, type a new word or select an item you desire in the list of existing keywords. Then press the Add button to move the keyword into the REN’s keyword list. To remove an item from the REN’s list of keywords, select one or more items you want to remove and press the Remove button.

When the information is correct, choose OK to save the enzyme and return to the Database Explorer.

Oligo operations

This section lists operations that are applicable to oligonucleotides only.

Edit

Use this operation to edit the selected oligo. Vector NTI displays the Oligo Editor dialog described below. You need to use the Rename command to change the oligo’s name.

New Oligo

Use this operation to create a new database oligo. The Oligo Editor tabbed dialog appears.

You may enter information about the new oligo as follows:

In the name box on the General Page, enter the name of the oligo.
In the Nucleotide Sequence box on the Oligo page you may enter or edit the oligo’s nucleotide sequence. Valid characters: ATUCG.
Use the DNA/RNA buttons on the Oligo page to select the oligo’s type.
To replace the oligo sequence with the complementary one check the Complementary box on the Oligo page.
In the Description box on the Oligo page, enter the oligo’s description.
Use the User Fields page to add custom data in a form of fields (see the User Fields section for details)
Use the Comments page to enter text comments.
Use the Keywords page to enter key words for the oligo. To add a key, type a new word or select an item you desire in the list of existing keywords. Then press the Add button to move the keyword into the oligo’s keyword list. To remove an item from the oligo’s list of keywords, select one or more items you want to remove and press the Remove button.

When the information is correct, choose OK to save the oligo and return to the Database Explorer.

Analyze Oligo

Use this operation to analyze a specified oligonucleotide The operation brings up the Analyze Oligo dialog box described in Chapter 13.

Analyze Oligo Duplexes

Use this operation to examine the duplexes of the highlighted oligo. The operation brings up the Oligo Duplexes dialog box, described in Chapter 13.

Gel Marker operations

This section lists operations that are applicable to gel markers only.

Edit

Use this operation to edit the selected gel marker. Vector NTI displays the Gel Marker Editor dialog described below. You need to use the Rename command to change the gel marker’s name.

New Gel Marker

Use this operation to create a new database gel marker. The Gel Marker Editor tabbed dialog appears.

You may enter information about the new gel marker as follows:

In the name box on the General Page, enter the name of the gel marker.
On the Gel Marker page, the Fragments list box lists by length all the fragments making up the marker. To add a fragment to the marker, enter its length in bp in the New Fragment box and press the Add button. The fragment is added to the list and the total number of fragments in the marker is increased by one. To remove a fragment from the marker, select it in the Fragments box and press the Delete button.
In the Description box on the Gel Marker page, enter the gel marker’s description.
Use the User Fields page to add custom data in a form of fields (see the User Fields section for details)
Use the Comments page to enter text comments.
Use the Keywords page to enter key words for the gel marker. To add a key, type a new word or select an item you desire in the list of existing keywords. Then press the Add button to move the keyword into the gel marker’s keyword list. To remove an item from the gel marker’s list of keywords, select one or more items you want to remove and press the Remove button.

When the information is correct, choose OK to save the oligo and return to the Database Explorer .

Copying Objects

The Copy/Paste operations are convenient shortcuts for database operations described in this chapter: subbase editing, shared database exchange (see below) and export/import.

Copy /Paste

This operations allows you to copy database objects between a) subbases of the same database, b) local and shared databases, and c) databases and the file system. When you copy the selected objects, their source and names are stored on the Clipboard. The Copy operation does not start data exchange; you must use the Paste command to put the copied data to a new place. The effect of the operation depends on where you paste the data. There are four possible scenarios:

the copied objects are pasted into the same subbase of the same database where they were copied. The Explorer treats this operation as an alternative way to duplicate copied objects (see the description of the Duplicate operation above).
the copied objects are pasted into another subbase of the same database where they were copied. In this case, the Explorer just includes the names of the copied objects into the target subbase; no object is modified or duplicated.
the copied objects are pasted into another database (local to shared or shared to local). The resulting actions are creating of the temporary archive for selected objects and importing it into the target database.
the copied objects are transferred from database to file system or vice versa. If you paste copied objects to the Windows 95/98 or Windows NT Explorer, Vector NTI Explorer automatically creates an archive file containing copied objects. If you paste files from the Windows Explorer to Vector NTI Explorer, the files are imported into the target database. Vector NTI Explorer is usually able to recognize the types of the pasted files automatically and take appropriate actions. When it cannot determine the type of imported files, it will show a dialog, allowing you to select the type or cancel the operation.

Note The Explorer transfers object data "on demand" only; meaning, when the actual data are requested to create objects outside the source database. This approach significantly reduces time-consuming data copying but may lead to unexpected results if objects whose names are copied on the Clipboard are deleted or modified before paste. Remember, that the actual data are collected when you paste data, not when you copy them.

Drag and Drop

You can also transfer objects by selecting them and "dragging" to another location using the standard drag/drop technique. The result of drag/drop is equivalent to copy/paste operations, the only difference being that drag/drop leaves the Clipboard contents unchanged. Vector NTI Explorer also supports right button drag/drop. When you drag the objects using the right mouse button, Vector NTI Explorer displays an action menu on the place of drop. This action menu contains two choices (Copy and Cancel) for database/file system and local/shared transfers. In case of transfer between subbases of the same database the third option (Move) is also available. The Move operation allows you to combine two operations: add selected objects to another subbase and exclude them from the current subbase. The Move operation is not available if the source subbase has its contents maintained automatically.

Explorer Options

You can customize the way information is presented in Explorer windows as well as Explorer’s preferences for molecule data exchange. Some settings like column size in the Details view (see below) are changed directly (by dragging the edge of a column). To change other settings you may need to choose the Options command from the View menu. All your settings are preserved between Vector NTI sessions.

When you chose the Options command, the Explorer displays the Options dialog, allowing you to change options related to the current database table. To set options for a table other than the active one, you need to switch to that table first.

Details View page

The Explorer’s database object pane can work in one of four view modes: Icons, Small Icons, List and Details (or Report). In the first three modes only object icons and names are displayed. The Details view mode also allows you to see the values of object fields; you may select what fields are displayed for each object type by choosing the desired fields in the Details View page. You may also change the order of columns and the text alignment of each column.

Status Bar page

This dialog page allows you to choose the type of information displayed in the status bar when there is a single selected object in the object pane. You can tell Explorer to show one of object fields or just use the "1 item selected" message.

Tips page

When you stop the mouse pointer over an object in the list pane of the Explorer for more than one or two seconds, Vector NTI can display a small message (a ‘tip’) containing information about the object under the mouse pointer. You can configure what is displayed on the Tips page. You can tell Explorer to show one of object fields or not to show any message at all.

Copy Molecule page (DNA/RNA Molecules table)

This page allows you to select the preferred file format for single molecule export (either via copy/paste or drag/drop to the file system or other programs). The available formats are: GenBank, EMBL, FASTA, Sequence and Vector NTI Archive. The Explorer allows you to choose between Vector NTI Archive format and FASTA format if more than one molecule is selected (see below).

Copy Molecules page (DNA/RNA Molecules table)

If more than one molecule is selected, the Explorer allows you to choose between FASTA format and Vector NTI Archive format for transferring the selected molecules to the file system target (either via copy/paste or drag/drop). If you chose FASTA format, only sequences of the selected molecules will be transferred. Vector NTI Archive format gives you more control in deciding what should be transferred. Since selected molecules can have parents that were not selected, something can be done to preserve the integrity of the created archive. This page allows you to select one of three possible options: a) expand the archive to include missing parents, b) disconnect copied molecules with missing parents and c) keep the "open" links to the missing parents. These options affect only the contents of the created archives; copying does not change database molecules.

Copy Molecule page (Protein Molecules table)

This page allows you to select the preferred file format for single molecule export (either via copy/paste or drag/drop to the file system or other programs). The available formats are: GenPept, SWISS-PROT, FASTA, Sequence and Vector NTI Archive. The Explorer allows you to choose between Vector NTI Archive format and FASTA format if more than one molecule is selected (see below).

Copy Molecules page (Protein Molecules table)

If more than one molecule is selected, the Explorer allows you to choose between FASTA format and Vector NTI Archive format for transferring the selected molecules to the file system target (either via copy/paste or drag/drop). If you chose FASTA format, only sequences of the selected molecules will be transferred. Vector NTI Archive format gives you more control in deciding what should be transferred. Since selected molecules can have DNA parents that were not selected, something can be done to preserve the integrity of the created archive. This page allows you to select one of three possible options: a) expand the archive to include missing DNA parents, b) disconnect copied molecules with missing parents and c) keep the "open" links to the missing parents. These options affect only the contents of the created archives; copying does not change database molecules.

Opening Explorer window at startup

Vector NTI can automatically open the local Explorer window for Molecule table at the time you start the program. To turn this feature on or off you need to use the Options command from the Edit menu of the main Vector NTI’s workspace window; look for the Open Local Explorer At Startup box on the General page of the Options dialog.

Sorting

You can sort the database objects by name or any of the fields, selected for display in the Details View page (even if the current view mode is not Details View). You can also select descending or ascending sorting order. In all view modes you can use the Arrange Icons submenu of the View menu; if you are in the Details view mode, you can click on the column header. Clicking on the same column header for the second time reverses the sorting order.

Database Reports

Vector NTI Explorer allows you to prepare reports on your database’s contents by generating report data suitable for popular word processing and spreadsheet programs. The first step in preparing a report is selecting the database table and object subset as described above. The right pane should contain all objects you would like to include in the report. If you do not have a subbase containing all objects you need, you can select them and create a new subbase or you can generate report on selected objects only. The next step is switching to the Details View mode and selecting a subset of objects’ fields to be displayed. This process is not specific to report generation; see the Vector NTI Explorer operations above for details. When you have all required fields selected, you can sort your objects by clicking on column’s headers. When you are satisfied with columns set, order and objects’ sorting order, select the Camera command from the Edit menu or press the Camera button on the Explorer’s toolbar (the last button to the right). The Camera dialog will allow you to choose what objects to include in the report (all objects from the current subbase or selected objects only) as well as the place to store the report information (the Clipboard or a file). After you saved the report information, you may switch to your favorite word processor, spreadsheet or database application and paste/import the report data there. Vector NTI prepares the report data in two formats: one is a plain text format with the TAB character used as column separator and the newline character as a row separator (sometimes called the "CSV" format); another is Microsoft Word’s Rich Text format (RTF). These formats can be pasted or imported in most popular office applications like Microsoft Word, Microsoft Excel, Claris File Maker Pro, etc. The simplest way to prepare a printed report is to paste the data into a new Microsoft Word document, select pasted table and format it to your liking using the Table AutoFormat command from the Table menu. The following sample report has been prepared using this procedure:

Name	Length	Storage Type	Modified	Record #
MyDesign 1	3697	Designed	09/27/96 06:11:01	14e
NEWMOLcc	8755	Designed	10/17/96 04:41:50	116
NEWMOL1		Constructed	09/26/96 12:52:43	145
NEWMOL@1	13292	Constructed		11c
CVACYCNMT	4943	Basic	09/18/96 07:36:50	129
pACYC177	3941	Basic		72
pACYC184	4245	Basic		73
pAM34	6000	Basic		74
pATH1	3779	Basic		76
SE	36	Basic	09/06/96 04:36:24	11b

Explorer Shortcuts

The Explorer offers many shortcuts that may make your work more productive:

Drag molecules from the local database Explorer window onto the main Vector NTI window to open several molecules in one step.
Open Windows Notepad and drag/drop a molecule on its window. The molecule will be displayed in the text format you chose for file system export (see Copy Molecule page in Explorer Options section).

Here is the list of useful Vector NTI Explorer keyboard shortcuts:

Shortcut

Action

F2

Rename

F3

Search

F4

Select table

F5

Refresh

F6 or TAB

Switch to another pane

Enter

Open selected object

Ctrl+Enter

Show Properties

New Object / Select Object Dialogs

Many features of Vector NTI Explorer are available in the New Object / Select Object dialogs appearing in many situations like opening a Molecule Display window, saving modified molecule to the database under a new name, etc. These dialogs display object lists in the same way the Explorer does; you can switch between Small Icons, List and Details view modes, chose object fields to be displayed in the Details mode, sort by any one of displayed fields and display the object properties dialog for selected objects. Since New Object / Select Object dialogs do not have menu bars, you need to use the right mouse button: right click on object or column header in the Details view mode displays shortcut menus with the Properties and Columns commands. The Properties command is also assigned to a button on a dialog toolbar, but the Columns command can be invoked only via right-click menu.

Contact Manager

Vector NTI is increasingly used as a communication tool for exchanging information between researchers. This is why Vector NTI maintains a contact list which you can use to store contact information about your colleagues. The Contact Manager is a tool for creating, updating, deleting and organizing contact records.

To launch the Contact Manager, choose the corresponding option from the Database menu. The Contact Manager dialog box appears:

The Contact Manager dialog box displays a list of all stored contact records. Many user interface features of the Contact Manager are similar to those of the New Object / Select Object dialog functioning in the Details mode. You can choose record properties to be displayed, sort by any one of the displayed properties and display the record properties dialog for selected objects. The New Object / Select Object dialog is described above in this chapter.

There are five operation buttons in the upper left corner of the Contact Manager allowing you to perform various operations on the contact records. To perform an operation on a contact record, you must first select the contact record in the contact list. The only exception is the Add New operation which does not require any records to be selected.

Operations on contact records

Add New

To create new contact record, press the Add New button. The User Information dialog box appears. Enter the coordinates of the person you would like to add to the contact list in the appropriate boxes. Only the Name box is mandatory for the new contact record. All other fields, such as the Telephone, Fax, E-mail, etc., may be left empty if you don't know the appropriate data. You may edit them later.

Edit

Press this button to edit a selected contact record. This command calls up the User Information dialog box loaded with the selected contact record:

When the editing is complete, choose OK to save the contact record and return to the Contact Manager.

Delete

Press this button to delete the selected contact record from the list. Vector NTI asks for confirmation before deleting the contact record.

Rename

Press this button to change the name of the selected contact record. The Manager displays a small edit box where you can change the name of the contact.

Properties

Press this button to display the properties of the selected contact record. Only indexed contact fields—Telephone and E-mail—will be displayed in the Properties dialog box. Use the Edit operation to view/edit the entire contact record.

User Field Manager

The User Field Manager dialog box maintains a list of User Field Definitions which are templates for adding extra data to database objects. Many user interface features of the User Field Manager are similar to those of the Contact Manager dialog described above in this chapter. You can choose User Field Definition properties to be displayed, sort by any one of displayed properties and display the User Field Definition properties dialog for selected User Field Definitions.

To launch the User Field Manager, choose the corresponding option from the Database menu. The User Field Manager dialog box appears:

There are several operation buttons in the upper part of the User Field Manager allowing you to perform various operations on the User Field Definitions. To perform an operation, you must first select a User Field Definition in the list. The only exception is the Add New operation which does not require any items to be selected.

Note, that you cannot use the name of a system field (see System Fields Table in the beginning of this chapter) as the name of a new User Field you define. If you really want to name your field ‘Default’, you can use ‘default’ or ‘DEFAULT’ (Vector NTI field names are case-sensitive).

Operations on User Field Definitions

Add New

To create new User Field Definition, press the Add New button. The User Field Definition dialog box appears:

In the Name edit box enter the name of the User Field. The User Field will appear under this name in the descriptions of database objects.

Choose the Type of User Field. A User Field may be of one of the predefined types:

String - arbitrary text string (including numbers),
Yes/No - binary field which may be set only to "Yes" or "No",
List of Strings - list of arbitrary text strings of any length,
One of Predefined Strings - field which may be set only to one of predefined text strings from a user-defined list,
List of Predefined Strings - field which may be set only to any subset of predefined text strings from a user-defined list,

Any User Field may be indexed and cached in the database tables. You can indicate that a User Field has to be cached by checking the Cache in Index Table check box. Cached fields will be accessed faster but will occupy more RAM in your computer. We recommend to cache only those fields which you often use, for instance, when viewing database objects in the Details mode of the Vector NTI Explorer or in the New Object / Select Object dialogs (see above). If you see that Vector NTI Explorer slows down when it shows the object’s fields in the Details View mode, you may call up the User Field Manager and ask Vector NTI to cache the fields you want to see in the Explorer. Cached and ordinary fields do not have any functional differences; you can turn this option on or off any time you need it.

Any User Field may have a default value or values that are presented to the user when he or she attempts to fill the previously blank field of the database object. Default is shown in the Default Values part of the dialog box. You may change the default by pressing the Change button.

The Predefined Values part of the dialog box is only enabled for fields of the One of Predefined Strings and List of Predefined Strings types. For those fields you have to enter one or more value strings to chose from. These values will be displayed as a list of available options when the user tries to fill or change the actual object’s fields. Use the edit box and the Add and Delete buttons to define the predefined values for the User Field.

The Description part of the dialog box allows you to enter an informal description of the field to help the user fill or edit the value of the field in a database object. The description you enter here will be displayed in the field value dialog for this field as well as the "tip" message displayed whenever the user stops the mouse cursor on the field name in the User Fields page of object editors (see below).

Note To save useful space on your computer’s screen and still allow you to see which predefined values are selected, you may define these values using the ‘abbreviated’ format: abbrev=full form as shown below (these are some of predefined values for a sample "Commercial Sources" field for enzymes):

A=Amersham Life Sciences-USB

B=Life Technologies Inc, Gibco-BRL

C=Minotech Molecular Biology Products

D=Angewandte Gentechnologie Systeme

Vector NTI displays only abbreviated form (for example A, B, D) in the Explorer windows and other places, but you will see the full forms in value-editing dialogs.

Edit

Press this button to edit a selected User Field Definition. This command calls up the User Field Definition dialog box loaded with the selected User Field Definition. When the editing is completed, choose OK to save the User Field Definition and return to the User Field Manager. Sometimes the editing will require updating database indices. Vector NTI will automatically recognize those situations and launch the appropriate procedure. Usually it takes less than a minute to update the indices.

Delete

Press this button to delete selected User Field Definition from Vector NTI’s Field Definitions list and, optionally, to delete field values from the database objects. Vector NTI asks for confirmation before deleting the User Field Definition. It also asks whether you want to delete the appropriate User Field values from all database objects. You may decide not to do that at that particular time: deleting only the User Field Definition will not affect consistency of the database information. When you delete the Field Definition from the list, Vector NTI will no longer prompt you to fill this field in new objects and existing objects where it was blank. However, unless you delete the field value from database objects, Vector NTI will still store and display the existing field data in the database objects. Remember though, that if you try to edit the existing value of that "unlisted" field in any database object, Vector NTI will ask you to add the definition of the field back to the User Field Definition List before proceeding.

Rename

Press this button to change the name of the selected User Field. The Manager displays a small edit box where you can change the name of the contact. After renaming a User Field Vector NTI will have to rebuild database indices to change the field’s name in all database objects, and will automatically launch the appropriate procedure.

Properties

Press this button to display the properties of the selected User Field Description. The properties displayed for User Field Descriptions can be also displayed in the User Field Manager dialog: right-click on the list header bar and select Columns command from the popup menu.

Import/Export

To simplify the maintenance of User Fields across several databases, Vector NTI allows you to save your User Field Definitions as "archives"—data files of special format—which may be transferred to another computer and read by Vector NTI running on that computer. That gives you the possibility to share your set of User Field Definitions with your colleagues, or to maintain the same set on several Vector NTI databases (for instance, at work and at home).

To export User Field Definitions to the archive, press the Export button. A dialog box appears allowing you to select the definitions to be exported. Select the required definitions and press the OK button. A standard File Save dialog appears. Indicate the directory and archive file name in which you would like to store the exported definitions. Press the OK button, and Vector NTI creates the archive.

To import User Field Definitions from the archive, press the Import button. A standard File Open dialog will appear. Indicate the directory and archive file you would like to read from. Press the OK button, and Vector NTI performs the import. After importing, Vector NTI will have to rebuild database indices, and will automatically launch the appropriate procedure.

Set In/Clear In

You may set a value or clear all values for a particular User Field in a group of database objects. This may be useful if you just created a new User Field Definition and would like to assign its values for all or some of existing database objects.

To set a value for a User Field, select the User Field and choose a subset of database objects from the database tree. You may choose all database objects regardless of their type or a particular subbase for database objects of a particular type (molecules, enzymes, oligos or gel markers). If you don't want to overwrite existing values of the User Field in the selected group of objects, check the "Do not overwrite..." box.

Then press the Set In button. A dialog appears allowing you to specify the value of the field to be set. Set the value and press the OK button. Vector NTI will give you a description of the action about to be performed, then after your confirmation, inserts the specified value into the specified objects.

To clear all values of a User Field, select the User Field and choose a subbase of database objects in the database tree. You may choose all database objects regardless of their type or a particular subbase for database objects of a particular type (molecules, enzymes, oligos or gel markers).

Then press the Clear In button. Vector NTI will give you a description of the action about to be performed, then after your confirmation, clears the values of the specified User Field in the specified objects.

If you want to set or clear fields in a set of individual objects not currently represented by an existing subbase, you may close the User Field Manager, create the required subbase in the Vector NTI Explorer and then return back to the User Field Manager. Alternatively, you may change field values in individual objects by editing them in the Explorer one by one as described below.

Editing User Fields in Individual Objects

When a User Field is defined in the User Field Manager you can fill it in any database object using the User Fields page of the appropriate object editor dialog.

User Fields page

The User Fields dialog page presents you with a list of all User Fields currently filled in the object being edited as well as the list of blank fields that are defined in the local User Field Definition list but are not yet filled in that object. You can fill or edit any field by double-clicking on the field name or selecting the field name and pressing the Change Value button. If the field you want to edit is not listed in the local User Field Definition list, Vector NTI will ask you to enter the field’s definition first. When the field definition is added to the local definition list, Vector NTI will display the appropriate field value dialog. To quickly clear any User Field of the object, select the name of the field and press the Remove Value button.

User Fields in Molecule Display Windows

Since molecule is most commonly used kind of Vector NTI database object, Vector NTI allows you to view and edit User Fields in the Text panes of Molecule Display windows. User Fields are listed in the top-level User Fields folder of the Text Pane. To edit a field, you may right-click on its line and select the Edit Field command from the shortcut menu.

Note Vector NTI 5.0 also supports an experimental advanced feature called hot links. Hot links are User Fields of special format recognized by Molecule Display windows. When you double-click on a hot link in the text pane of a Molecule Display window, Vector NTI tries to invoke the appropriate Vector NTI Tool (see Chapter 17) with the field value as a tool argument. To be recognized as a hot link, the User Field should be of the String or One Of Predefined Strings type and the field value (a string) should have the following format: type:data (a string with colon character separating link type from link data). When you double click on such a field, Vector NTI tries to invoke a tool named "Open Link|type" (i.e., a tool listed under title "type" in the Open Link submenu of the Vector NTI Tools menu). The tool should have Input Type set to "Link Data"; "%1" characters in the tool definition command are substituted to the data part of the hot link. Vector NTI Demo provides an illustrative example: CVACYCNMT molecule contains a hot link to its WWW Source (GID:U25270); clicking on it invokes the Open Link|GID tool that retrieves the original molecule from NCBI’s WWW Entrez server. Other possible uses of hot links include WWW links (like URL:http://myserver.com/mypage.html) or local documents or pictures (DOC:mydoc.txt). Vector NTI tools supporting these idioms will be published on InforMax’s WWW site (http://www.informaxinc.com) in the section dedicated to Vector NTI tools.

Shared Databases

Vector NTI allows you to create and access special databases which may be used as repositories of DNA/RNA or protein molecules, enzymes, oligonucleotides, and gel markers shared between several Vector NTI users on a network. Shared databases give you the same flexibility and control as Vector NTI archives (including automatic consistency checks for constructed molecules) but they are much more convenient for groups of people which already use a computer network to exchange information and store common data.

Shared databases are not a replacement for local databases; each Vector NTI application still must have its own local database. The local database is used in all operations: construction, design, creation of viewers etc. The local database is also the place where you store private and temporary data. The main purpose of the shared database is to store common data; the only kind of operations you can perform on shared database is copying data to/from the local database, various database management operations (creating and deleting subbases etc.) and database searches. For instance, you may copy some of your molecules and enzymes from your local database into the shared database. In order to use them in the design process, your colleague must copy them to his/her local database first.

In addition to biological data, each database contains information about its creator and registered users. Only the creator and registered users can have access to database data. The database creator can also change database properties, remove registered users, and define the password required to become a register user.

Note Vector NTI shared databases use portable data format and file naming conventions to ensure that both Macintosh and Windows users of Vector NTI can access common databases. Shared databases can be located on a wide range of file servers—Vector NTI can work using not only services native to each system, (Microsoft Network or AppleTalk) but also various Unix (NFS or Samba) and NetWare services.

Creating a new shared database

To create a new shared database you should have an administrative version of the Vector NTI application and Vector NTI network license. A network license allows you to create any number of shared databases but it also limits the number of users for each database you create. Each user should have a Vector NTI application version 3.1 or later to access shared databases.

Before you start creating a shared database you should find a place on your network (a computer, storage volume and directory or folder) where the database will be located. This location should be accessible from the computers of all potential users of the database—users should be able to connect to this location or mount the corresponding network drive and have read/write/delete permissions for all files in database directory and its subdirectories. Good places for shared databases are file servers which can be "visible" as storage devices to other computers in a network. Vector NTI requires that a separate empty directory should be created for each shared database.

When you arranged the network directory for a new shared database, choose the Shared Database command from the Database menu. The Connect To Shared Database dialog appears.

In this dialog you can perform a number of database management operations: create new database, find location of the existing database, and edit database properties and user information.

Press the Create New Database button. A dialog box appears asking you to enter your network license number. Type in the number and press OK. If the license number is valid, Vector NTI displays the standard File Save dialog box where you may select a location for the shared database definition file (dbdef). Find the empty directory you prepared on the previous step and press the OK button (Windows) or Save button (Macintosh). The database definition file is created; Vector NTI displays Database Properties And Users dialog where you can provide additional information for the database users:

In the Database Name box you should enter the name of the new database. This name will be displayed in all dialog boxes and messages related to the database.

Enter a registration password into Password Required To Register At Login box. Only those users who know the password will be able to become a registered user of this database. If you decided that the password is not necessary you can leave this field blank. If the password is not blank, Vector NTI will ask you to confirm the password before you leave the dialog.

When you are finished press the OK button. Vector NTI writes the data you entered into the database definition file and creates the files and directories required to store the database data. The database you just created has no registered users. To be registered, a user should login to the database and enter the registration password you specified in the Password Required to Register at Login box. This procedure is described in details below.

Note If anything goes wrong at this stage, check the network connection and make sure that you have write permissions for the chosen directory. Then, delete all files in the directory and repeat the last step.

In the Connect To Shared Database dialog box you will see the name and location of the database you just created.

Finding the location of an existing shared database

If you are going to use an existing shared database you should specify the location of the database. First, make sure that you have a working network connection to this location or that the corresponding network drive is mounted and you have read/write/delete permissions for all files in the database directory and its subdirectories.

Note On some systems you can mount network drives from the standard File dialogs. In this case, no separate step is required.

Open the Connect To Shared Database dialog box and press the Find Database button. Vector NTI displays the standard File Open dialog box where you should find the shared database definition file (dbdef). Find the database directory and press OK button (Windows) or Open button (Macintosh). Vector NTI tries to read the database definition file; if it succeeds, you will see the name and location of the database in the Connect To Shared Database dialog box.

Editing database properties and user accounts

When the location of a shared database is specified and you are the creator of this database, Vector NTI allows you to edit the database name and registration password. The creator of the database can also remove registered users. To edit database properties and user account information press the Edit Database Properties and User Accounts button. The Database Properties And Users dialog appears, allowing you to modify the corresponding database information.

Saving the connections in a connection profile

When the location of a shared database is specified you can enter login information that will be displayed to other users of a shared database. This is a good way to communicate your personal information such as name and phone number. When you are logged into a shared database, Vector NTI displays this information in addition to the login time and the information about your computer to other database users attempting to log in. In order to return to this configuration later you may save both database location and login information in a connection profile. Press the Save Connection As button and enter the name of the connection in the Save Connection As dialog box. Vector NTI stores the connection profile in the preference file; each time you open the Connect To Shared Database dialog box you see the stored connections list near the top of the dialog box. You can select stored connections from this list; to delete the connection from the profile you may press Remove Connection button.

Connecting to a shared database

When the location of a shared database is specified, Vector NTI allows you to connect to the database. In order to connect, press the Connect button. Vector NTI reads the information about the database creator and registered users. If you are not a creator or registered user of the database and the database limit of registered users in not reached, Vector NTI displays the dialog allowing you to register:

To register, choose Yes. If the user registration is protected by registration password, you will be asked to enter the registration password in the Login Registration dialog. If the password is correct, Vector NTI will add you to the list of registered users of the shared database.

If you are the database creator or registered user, you have full access rights to the database data. However, if you are not going to write to the shared database this time, you can check Read Only box. This will guarantee that the shared database contents will not be accidentally modified.

If you are not the database creator or registered user, you can choose to connect to the database in a browse-only mode to look at the database contents.

Note If Vector NTI cannot access the database at this or the subsequent stages, check the network connection and make sure that you have write permissions for the files in database directory and its subdirectories.

Managing a shared database

When your connection to the selected shared database is established, Vector NTI opens a separate Database Explorer window for the shared database. This window is a close functional equivalent of the local Database Explorer window: you can Search the database, manage subbases, rename and delete objects etc. However, the concept of Vector NTI’s shared databases prevents you from manually creating new objects in shared databases, opening Display Windows for objects stored in shared databases and editing shared database objects in place using object editor dialogs. If you want to modify a shared database object, you need to copy it to your local database, modify it there and put the modified copy back into the shared database as described in the next section. Note, that if the original object was submitted by somebody else, Vector NTI will not replace it, creating a separate object instead. This new object will have the same name but different "Submitted by" field, containing the Author Name you used to identify yourself in the Author Information dialog.

Exchanging data with a shared database

Vector NTI allows you to exchange data between your local and shared databases in a simple and intuitive manner. All you need is to open two Explorer windows (one for local and another for shared database), then copy data between them using drag-drop or copy/paste operations described in the Copying Objects section. The simplest way to start data exchange is to use the Local/Shared Data Exchange command from the Database menu of the Vector NTI main or Explorer window. This command allows you to choose a shared database, connects to it (as described in the previous sections), opens the shared database Explorer window and the local Explorer window (if needed) and then tiles two Explorer windows on your screen.

Vector NTI allows you to put your objects into a shared database without worrying about possible name conflicts with objects placed there by your colleagues. Vector NTI automatically stores the name you used to identify yourself in the Author Information dialog with the objects you put into a shared database. This name is stored in the shared database as a special "Submitted by" field of an object (it can be different from both the Author and Original Author fields of the object). Besides that, Vector NTI automatically creates and maintains special subbases containing objects that were submitted by the same users. The name alone is no longer a unique way to identify an object in the shared database; two or more different objects can have the same name provided that they came from different sources.

Disconnecting from a shared database

When you are finished exchanging data in the Shared Database Exchange dialog, press the Close button. You will be disconnected from the shared database and the database may be used by another user.

Summary

This chapter discussed database operations in Vector NTI. It covered the following topics:

Information stored in the database
Backing up and restoring the database
Managing subbases
Vector NTI archives
Molecule Database search
Database Explorer
Working with database DNA/RNA molecules
Working with database protein molecules
Working with database restriction endonucleases
Working with database oligonucleotides
Working with database gel markers
Managing contact records
Managing user-defined fields
Working with Shared Databases

Database object fields

Database object fields

Vector NTI archives

Vector NTI archives

Database Search

Database Search

DNA/RNA Molecule database search

DNA/RNA Molecule database search

Protein database search

Protein database search

Enzyme database search

Enzyme database search

Oligo database search

Oligo database search

Gel marker database search

Gel marker database search

Backup, Restore and Cleanup

Backup, Restore and Cleanup

Removing molecules from a subbase.

Removing molecules from a subbase.

When you are done editing a subbase.

When you are done editing a subbase.

Dismiss Subbase

Dismiss Subbase

Clear Subbase

Clear Subbase

Delete Contents

Delete Contents

Subbase Summary

Subbase Summary

Subbase Properties

Subbase Properties

Import Objects From Directory of Text Files  XE "  (molecules and oligos only)

Import Objects From Directory of Text Files  XE "  (molecules and oligos only)

Export All Subbase Objects Into Directory of Text Files (molecules and oligos only) )

Export All Subbase Objects Into Directory of Text Files (molecules and oligos only) )

Import Molecule From Text File  XE " 

Import Molecule From Text File  XE " 

Format for ASCII sequence files

Format for ASCII sequence files

Import Enzymes From REBASE Database

Import Enzymes From REBASE Database

Export Selection into Archive

Export Selection into Archive

Delete from Database

Delete from Database

Properties

Removing molecules from a subbase .

Removing molecules from a subbase .

Import Objects From Directory of Text Files XE " (molecules and oligos only)

Import Objects From Directory of Text Files XE " (molecules and oligos only)

Import Molecule From Text File XE "

Import Molecule From Text File XE "