Software review
Vector NTI, a balanced
all-in-one sequence
analysis suite
Abstract
Keywords: sequence
analysis, software package,
database, virtual cloning,
sequence assembly
Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis
and biological data management. It has a centralised database and five application modules:
Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the
features and functions available in this software are examined. These include database
management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular
viewer and internet tools. Some problems encountered when using this software are also
discussed. It is hoped that this review will introduce this software to more molecular biologists
so they can make better-informed decisions when choosing computational tools to facilitate
their everyday laboratory work. This tool can save time and enhance analysis but it requires
some learning on the user’s part and there are some issues that need to be addressed by the
developer.
INTRODUCTION
During the last two decades a variety of
computer programs (or packages) have
been developed for molecular sequence
analysis. Most of them are freeware,
which greatly benefits researchers with
limited budgets and bioinformaticians
who want to access source codes to
modify and/or integrate them into other
tools. However, free software to some
extent lacks integration with other
functions, and many do not have a userfriendly graphic interface.1 Commercial
software packages, on the other hand,
usually incorporate many functions, have
easy-to-use user interfaces, and offer user
support. Many bench scientists thus prefer
to use a single all-in-one commercial
software package despite their much
higher costs.2
Vector NTI is an integrated desktop
application for molecular biologists. It
was recognised as the best 2003
sequence analysis software by BioScience
Technology readers.3 Although Vector
378
NTI has been reviewed previously,4,5
these reviews were based on the old
versions. At least two more versions
have been released since then, with
current versions being Vector NTI
Advance 9.0 for Windows and Vector
NTI Suite 7.1 for Macintosh platforms.
In addition, InforMax was acquired by
Invitrogen6 in late 2002, and Invitrogen
has added some new features into
Vector NTI (eg Gateway Cloning). The
Vector NTI User’s Manual is helpful.
However, its huge volume (eg 694
pages for Vector NTI Advance 9.0) to
some extent holds back molecular
biologists’ intention to use this package.
The authors of this review have been
offering a bioinformatics tutorial course
and Vector NTI workshops to faculty,
staff and students at the University of
Nebraska-Lincoln. Many who took our
courses recognise Vector NTI as a
comprehensive and user-friendly
sequence analysis package. In this review,
useful features as well as some problems
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Software review
found in Vector NTI are discussed for
both Windows and Macintosh platforms.
THE SOFTWARE
Overview
Vector NTI Advance (or Vector NTI
Suite) consists of a central database and
five application modules. The database
provides an interface to access all
application modules. The following
modules are available: Vector NTI for
sequence creation, mapping and analysis;
AlignX for multiple sequence alignment;
BioAnnotator for nucleotide and protein
sequence analysis; ContigExpress for
sequence assembly and sequencing project
management; and GenomBench for analysis
and annotation of reference genomic
DNA sequences. In Vector NTI Suite for
Macintosh, GenomBench does not exist
and BioAnnotator is called BioPlot.
Vector NTI installation
Vector NTI software can be downloaded
from the Invitrogen web site.6 Free
registration is required for downloading.
The minimal system requirements for
Vector NTI Advance 9 are Microsoft
Windows 98 SE or above, 500 Mb HD
space, 128 Mb RAM and Microsoft
Installer Version 2. The minimal
requirements for Vector NTI Suite 7.1
for Macintosh are Mac OS X v. 10.2 or
above, Power Mac G3 or G4, 450 Mb
HD space, and 256 Mb RAM.
A single Vector NTI database can be
installed and shared by multiple users.
Each user can also create a unique
database in a separate location. Three
types of licences are available: trial, static
and dynamic. A trial licence gives the user
a fully functional copy of the software free
for 20 days.
Vector NTI database
Vector NTI uses the database and graphic
user interface, namely Database Explorer
(Vector NTI Explorer for Macintosh), to
manage data (Figure 1). This ‘database’
concept is the first thing the first-time
Figure 1: Vector NTI
Database Explorer
window
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users need to get used to. It has both
advantage and disadvantage. Using the
‘database’ concept is good for a large-scale
data management. On the other hand, if
you want to do a small job quickly, you
will be frustrated until you become
familiar with the way Vector NTI wants
you to manage your data. Before you can
start creating your own sequence file and
start any analysis, at a minimum, you need
to understand some terminologies such as
main database, sub-bases and objects. The
database consists of seven types of objects:
DNA/RNA molecules, protein
molecules, enzymes, oligos, gel markers,
citations and BLAST results. Vector NTI
Advance has also ‘analysis results’ object.
The user creates new sub-bases to archive
records on, for example, molecules
created in the laboratory, enzymes stored
in a laboratory freezer, or literature
collected for a research project. The
Explorer makes it relatively simple to
manage and manipulate various kinds of
data. With the Explorer, the user can
create and edit molecules, perform
database searches, import and export data,
create archives of molecules and analysis
results to share with other users. Vector
NTI takes into consideration general
security by providing database backup and
restoring functions. On the other hand, to
avoid quickly filling up the disk space and
cluttering the work space, it is suggested
that the user cleans up the database
regularly.
When you start Vector NTI for the
first time after installation, Vector NTI
creates an empty database. The user can
choose to import an initial set of database
objects from Vector NTI archives that
include a large number of samples of
DNA molecules, proteins, enzymes,
oligos and gel markers.
Molecule Display
The Molecule Display window, also called
Molecule Viewer, is the primary interface
to display and manipulate DNA/RNA
and protein molecules in the module
Vector NTI (Figure 2). It has a three-pane
format: Text pane containing molecule
information (eg general description,
feature map, original author) in
hierarchical folders, Graphics pane that
graphically displays the data in the
Figure 2: Molecule
Display window for a
DNA molecule, PBR322
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molecule file, and Sequence pane with the
primary sequence of the molecule. The
three panes are integrated to reflect each
other’s actions. For a protein molecule,
instead of Restriction Map folder as shown
in Figure 2, Analysis folder is automatically
created in the default setting in the Text
pane. It includes molecular weight,
isoelectric point and other
physicochemical properties.
With the Molecule Display window
opened, you can load and edit the
sequence and features, and perform
various types of analysis such as
polymerase chain reaction (PCR) primer
design and molecule construction as
described in the following sections. The
Vector NTI module has some basic sets of
tools such as creating a reverse
complement molecule, finding open
reading frames, translating a region or the
whole DNA molecule, searching motifs
and finding restriction enzyme sites. The
Restriction Report function available in
Vector NTI Advance (not in Vector NTI
Suite) produces a list of non-cutting
restriction enzymes. It does not have an
option to generate other types of lists: for
example, a list of single cutting restriction
enzymes. If you see an asterisk appearing
in a window title after the name of the
molecule as in Figure 2, the molecule has
been modified and needs to be saved in
the database if the user wants to keep the
changes. The asterisk was not observed in
Vector NTI Suite for Macintosh,
although the user manual described it so.
At times Vector NTI seems to make
some simple tasks unnecessarily tedious.
For example, in order to create a reverse
complement strand, you would think that
just a simple click on a tool button would
do the job. On the contrary, you need to
open the Molecule menu, find the
Operations submenu at the bottom, find
again Advanced (DNA/RNA) submenu,
and finally choose Make Reverse Copy to
create a new file. Calculating the sizes of
restriction fragments based on a particular
set of restriction enzymes found by the
Restriction Sites search function also
requires multiple steps.
Another shortcoming found is that it
supplies no flexibility in saving the
graphic file. The Camera function is used
for this purpose. It provides options
‘Picture Files’ (the PICT format for
Macintosh) and ‘Windows Meta Files’
(for Windows). Macintosh OSX users
have another option for saving the file in
PDF format using OSX’s Print function.
However, considering one reason to use
Vector NTI would be for its graphic
representation ability for molecular data,
better compatibility with commonly used
graphics software should be incorporated.
Designing primers for PCR and
sequencing
Vector NTI can design primers for PCR,
hybridisation probes and sequencing.
Vector NTI takes into account almost all
parameters that may affect the primer
selection, which include parameters
related to primer (eg melting temperature,
Tm , and percentage GC), amplicon,
structure, pairs, similarity, 39 end,
uniqueness, qualities and filters. It may not
be easy for a novice to decide which values
to set up with. In many cases, however,
the default values seem to work just fine. A
freeware Primer3,7 for example, has been
extremely useful in primer selection.
However, Vector NTI offers some more
attractive functions not found in other
programs, which include designing
primers for long PCR, alignment PCR
and multiplex PCR. Moreover, PCR
products can be saved to the database and
used for molecule construction.
Molecule construction
The greatest strength of Vector NTI
Advance and Vector NTI Suite lies in the
plasmid construction. It is easy to create
new molecules in Construction or Design
modes. Construction takes the regular
way of cloning; ie the user determines all
the steps to be taken, which include
defining the clone vector and inserts,
choosing restriction enzymes, and
selecting the methods of terminus
modification. In the Design mode, new
molecules can be created with the aid of
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Vector NTI built-in biological
knowledge. The users need only define a
list of donor and recipient fragments; the
choice of restriction sites and terminus
modification is left for Vector NTI to
decide. The Design process generates a
new molecule as well as a construction
plan, which describes the best possible
restriction sites and recombinant strategy.
One important feature of the molecule
design process is that the construction
plan can be adjusted based on specific
needs of the user by changing certain
options. For example, the user may
permit partial digests for constructing new
molecules.
The Fragment Wizard of Vector NTI
provides a step-by-step guideline in
defining a new molecule fragment,
making the process of adding fragments
quick and easy. The user can ‘reconstruct’
a previously constructed molecule using
the shortcut menu (right-click the
molecule file) in the Database Explorer
window. This Reconstruct feature is
useful for constructing molecules that are
similar to a previously constructed
molecule and for reconstructing
molecules that have failed a previous
construction attempt.
BioAnnotator (BioPlot for
Macintosh)
The BioAnnotator module enables the
users to perform various basic DNA/
RNA and protein sequence analyses,
displaying the results as linear graphics in
the Graphics pane (Figure 3).
BioAnnotator contains eight DNA/RNA
analyses (eg GC content and melting
temperature) and 50 protein analyses (eg
antigenicity, hydrophobicity and
polarity). Many of these analyses are
related to each other. However, beyond
providing a list of references in the
manual, there is no description for each
method, and users are left to speculate
what those plots mean. For example,
there are both GC content plot and
nucleotide frequency distribution plot.
How these plots are different (if they are)
is not explained.
AlignX and AlignX BLOCKS
AlignX is the Vector NTI module that
performs multiple sequence alignments
and displays them with easily interpretable
multi-colour graphics (Figure 4). Based
on the popular Clustal W algorithm,8
AlignX incorporates features including
profile alignment, secondary structure
Figure 3: BioAnnotator
window
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Figure 4: AlignX
window
consideration, automatic consensus
calculation, graphic display of a
phylogenetic tree, dot matrix comparison
and some alignment editing capabilities.
The AlignX Display window is divided
into four panes: Text pane for the
description of each molecule included in
the alignment project, Phylogenetic Tree
pane for a phylogeny, Graphics pane to
view plots of various types of analysis (eg
alignment quality) and Alignment pane to
display aligned sequences and the
consensus sequence. The main features of
AlignX are derived from a freeware
Clustal X (the graphic and enhanced
version of Clustal W).9 Two
improvements over Clustal X are the
ability to display the neighbour-joining
phylogeny graphically and the dot matrix
for pairwise alignments. For both
functions, separate software programs are
required for Clustal X users.
AlignX also allows the user to perform
very basic manual alignment editing by
shifting the position of gaps. What AlignX
misses is Clustal X’s flexibility to align only
selected regions or molecules directly in
the existing alignment. AlignX’s profile
alignment is limited and only one
sequence or existing alignment can be used
as the profile (a sequence or alignment for
other sequences to be aligned against).
AlignX supports only one alignment
format, ie MSF format. In order for better
compatibilities with other alignment and
phylogeny programs, at a minimum,
FASTA, Clustal W, PHYLIP and NEXUS
formats need to be supported.
AlignX BLOCKS is an independent
program available in the AlignX
module. It analyses and identifies
localised sequence similarities (called
blocks) among multiple protein
sequences (Figure 5). It is an interesting
tool. It will be useful for examining
conserved regions, identifying functional
domains and presentation of domain
structures. It would be more useful if we
were able to perform BLAST or Pfam
search based on the block sequences
identified. One small problem is in the
use of words ‘link’ and ‘unlink’ in the
Blocks menu (the AlignX menu for
Vector NTI Suite). At first we thought
simply that their functions are to link/
unlink domains along the sequence.
They are used, however, for ‘aligning’
domains (blocks) vertically across
multiple sequences. Figure 5 shows a
‘linked’ block alignment.
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Figure 5: AlignX
BLOCKS window
Sequence fragment assembly
(ContigExpress)
The ContigExpress module allows the
user to assemble small fragments in text or
chromatogram formats into longer
contiguous sequences, ie contigs (Figure
6). The user needs to first create a
ContigExpress project in order to work
with ContigExpress. ContigExpress can
recognise files in formats of GenBank,
FASTA, ABI, SCF and some others.
Surprisingly, it does not support the
Applied Biosystem’s ABD format.10 The
user needs to use, for example, the Staden
package11 to convert the ABD format to
the SCF format before the file can be used
with ContigExpress. Fragments with
chromatograms can be edited directly and
Figure 6: Contig
Viewer window
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their changes can be tracked. Two
methods, ‘pairwise’ and ‘linear’, are used
for assembly. The User’s Guide explains
that the pairwise assembly is best for
assembling 10 or fewer fragments whereas
the linear assembly is good for assembling
11 or more fragments. Similar to what
was mentioned earlier, is that the
algorithms used in these two assembly
methods are not described. If the
algorithms are available, it would help
users understand their assembly results and
compare them with other methods. The
contigs can be saved in a GenBank,
EMBL or FASTA format file.
One important feature of
ContigExpress is that it has many
trimming functions for preassembly
processing. These include vector
contamination trimming, end trimming
and Phred quality values trimming.
GenomBench
GenomBench is Vector NTI Advance’s
genome project application. There is no
Macintosh version yet. In GenomBench,
the user can search, retrieve and store data
from several principal Distributed
Annotation System (DAS) servers such as
UCSC 12 and Ensembl.13 GenomBench
has a multi-pane interface including
Overview pane, Info pane and Feature
Map pane (Figure 7). GenomBench
allows the user to search public databases,
edit sequence and graphics, import and
export annotated sequences, and send
annotated sequences to Vector NTI. It
also provides a means for mapping
sequences onto genome regions using
Sim414 or Spidey15 genome alignment
algorithms. GenomBench maintains its
own local database for storing sequences
and analysis results, which is independent
from the Vector NTI database.
GenomBench provides a seamless
access for desktop computers to the DAS
servers. Its application, however, is
limited in that not many public DAS
servers are available in default. The users
need to create custom connections by
themselves in GenomBench. Most
genome-related DAS servers provide
reference information only for model
organisms. Certainly it would not
provide much benefit to researchers who
are working on non-model organisms.
More functions (eg gene prediction)
need to be integrated in order to serve
for the general needs of genome
projects.
Figure 7: GenomBench
window
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Internet tools
Vector NTI takes a full advantage of
internet. NCBI BLAST 16 similarity
search is fully integrated into Vector
NTI’s graphic interface. It has its own
dialogue window to manage various
search options and BLAST Viewer to
view the BLAST results graphically. One
function that should be incorporated is
the option to generate a multiple
alignment quickly with the selected hit
sequences. Several protein sequence
analyses (eg NNPREDICT, TMpred),
similarity search (eg PSI-BLAST) and
pattern search (eg BLOCKS, PROSITE)
can be accessed directly from the Vector
NTI interface. The PFAM interface is
available only on the Windows version.
PubMed/Entrez Search is another Vector
NTI’s graphic interface program for the
popular NCBI search tool. With Citation
Table of Database Explorer and Citation
View, Vector NTI provides a practical
bibliography management tool complete
with more than 50 journal reference
styles, although the style selection has a
strange preference (eg Nature, Cell and
Proc. Natl Acad. Sci. USA styles are
missing). Obviously all of these internet
tools share the possible problems in
networking connection and
reorganisation of remote links. Frequent
updates will be needed.
3D molecular viewer (3D-Mol)
3D-Mol is a stand-alone program
included in Vector NTI. It can generate a
graphic presentation of three-dimensional
structures downloaded from the PDB
(Protein Data Bank).17 3D-Mol has many
basic presentation capabilities with a
simple clean interface. It has more
flexibility than Cn3D18 (freeware by
NCBI). For example, 3D-Mol has a few
useful functions as calculating distances
and angles between atoms. Although it is
not as powerful as Swiss-PDBViewer,19
simply as a visualisation tool, 3D-Mol is
sufficiently good and an easy-to-use
software. On Macintosh, 3D-Mol
requires the ‘millions’ colour mode – it
did not run with the ‘thousand’ colour
386
mode. Only one graphic format (BMP
both for Macintosh and Windows) is
supported to save 3D images.
Customising tools (Tools
Manager)
Vector NTI provides Tools Manager for
customising items included in some
menus. Tools Manager allows users to add
new menu items to open internet links,
start internet tools, or run programs and
scripts. Because the number of internet
links and tools included in Vector NTI is
limited, this customisation capability is a
welcome addition. It means Vector NTI
could grow with users based on their
specific research fields.
CONCLUSION
Computational tools and databases are
essential for discovering knowledge
embedded in the exponentially growing
volume of biological data. Many sequence
analysis suites such as GCG 20 are simply a
collection of computer programs, each
with individual input and output files, and
it is not easy to manage different types of
data and outputs. In this aspect, Vector
NTI is unique and the Database Explorer
provides a simple interface to manage and
manipulate various types of data. The user
can create new sub-bases to organise data
used for different experiments and
research projects. Vector NTI also has a
good graphics presentation capability.
Restriction maps and other figures can be
quickly and nicely generated in Vector
NTI.
Vector NTI was also found to have
several drawbacks. As mentioned earlier,
it takes time for the first-time users to
become familiar with the organisation
structures. The use of its database system
certainly makes the learning curve steep at
the beginning; sometimes unnecessarily
so. The Database Explore program
integrates other modules through its
menus. However, the opposite direction
of integration is not supported. Once the
users are in the AlignX module, for
example, coming back to the database
window is not easy, especially after
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opening many windows and modules.
Adding a database icon on the tool bar of
each module or adding a link to the
database in each Window menu should
solve this problem easily. Some of the
programs such as dot matrix are only
available in certain programs; some of the
programs such as Alignment PCR are not
very visible to the users. Some menus and
submenus are confusing (eg editing
restriction map via the menu View instead
of Edit). In terms of display, some icons
are too small (eg the icons ‘+’, ‘–’ in the
Analysis List Setup window in
BioAnnotator).
Vector NTI can create a system
administration nightmare quickly. After
some hours of sequence analysis, users
may, without knowing, end up running
many different programs. All individual
modules and related programs need to be
closed one by one manually when users
finish their work. This becomes a serious
problem if the institution maintains a
limited number of dynamic licences. A
clean-up process should be incorporated
when users log out or quit. Additionally,
the manual should include the detailed list
of available functions, so that users can
find the necessary function easily. Instead
of a single large manual, the tutorials and
reference sections can be divided into two
volumes. The reference part should
include descriptions of each method
instead of just giving a citation list. A
comparison table of included functions
between Windows and Macintosh
versions should be provided on the web
site. The number of supported output file
formats needs to be increased especially
for graphics formats. Finally, it would
help first-time users if a template user
database were created at the initialisation
process in addition to the one containing
all the examples. They would then not
have to search their files from the large
number of example files the installer
copies during the installation process.
Although it still has some problems and
improvements are necessary, our overall
impression is that Vector NTI is a wellbalanced integrated software package.
Although the price is at the high end, at
around US$1,500 for a single copy licence
(plus US$500 for technical support), it
comes with almost all basic computation
tools routinely used in any molecular
biology laboratory. It even includes a 3D
viewer as well as a bibliography
management program. Except for its nice
graphics and bibliography capability, the
majority of the functions have equivalent
freeware available through internet
(BLAST/PubMed server, Clustal X,
Primer3, Swiss-PDBViewer, etc), and
many more powerful programs are
available through various web servers.
However, for the laboratories and users
who prefer to use a fully integrated
environment without worrying about
installing and using different software for
each different task, and who are willing to
learn and take the advantage of using an
organised database system, this is a good
package. With its customisable menus, the
users can also incorporate their favourite
tools if they are not supported in Vector
NTI. Prospective users should take the
advantage of the free trial licence, and
spend some time to browse through the
manual to see if the high cost and longer
learning time are worthwhile for the
functions it offers.
Acknowledgments
The authors were supported by the NSF EPSCoR
program (EPS-0091900). G. Lu is also supported
by the NSF EPSCoR program (EPS-0346476) and
the INBRE Program of the National Center for
Research Resources (P20 RR16469).
Guoqing Lu,
School of Biological Sciences and Center for
Biotechnology,
University of Nebraska-Lincoln,
Lincoln, NE 68588, USA
E-mail: [email protected]
Etsuko N. Moriyama,
School of Biological Sciences and Plant Science
Initiative,
University of Nebraska-Lincoln,
Lincoln, NE 68588, USA
E-mail: [email protected]
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spidey/).
16. NCBI BLAST (URL: http://
www.ncbi.nih.gov/BLAST).
17. Protein Data Bank (URL: http://
www.rcsb.org/pdb/).
18. Cn3D (URL: http://www.ncbi.nih.gov/
Structure/CN3D/cn3d.shtml).
19. Swiss-PDB Viewer (URL: http://
us.expasy.org/spdbv/).
20. Saisanit, S. (2003), ‘GCG sequence analysis’, in
Krawetz, S. A. and Womble, D. D., Eds,
‘Introduction to Bioinformatics: A Theoretical
and Practical Approach’, Humana Press,
Totowa, NJ, pp. 315–321.
& HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 5. NO 4. 378–388. DECEMBER 2004