Transcript Introduction to Vector NTI Advance 10

Introduction to Vector NTI Advance 10
Yi-Bu Chen, Ph.D.
Bioinformatics Specialist
Norris Medical Library
University of Southern California
323-442-3309
[email protected]
June 29, 2007
Workshop Outline
 Overview of Bioinformatics Support at NML
 Vector NTI Advance 10 Suite Overview
 Vector NTI Database Explorer Overview
subset operation
data export/import, data search
database backup and migration
 Vector NTI Key Functions Overview
Display setup, graphics editing
Import/Create new sequences
Analyze Sequences: PCR primers design
Analyze Sequences: restrictions and mutagenesis
Analyze Sequences: translation and back-translation
 ContigExpress Overview
 AlignX Overview
Vector NTI Advance 10 Download and Installation
1. Navigate to the Vector NTI 10 web page at NML
insert the web link here
1. Download and print out the “Vector NTI download
and installation instruction” file
2. Follow the instruction to register, download, install
and license the Vector NTI 10 suite
3. Confirm the installed software in fully functional
mode
4. Contact Yi-Bu if you experience any problems
Main Modules of Vector NTI Advance 10 Suite
Vector NTI
 Center module, provides access to all other modules via its integrated interface
 Sequence creation, mapping, analysis, design, annotation, illustration, gel simulation,
Align X
 Multiple sequence alignment of proteins and DNAs, alignment editing and visualization
 Create profile alignment using selected sequences; use standard or user-defined substitution matrix
 Secondary structure consideration; dot matrix comparison of two sequences; GCG and .msf file conversion
ContigExpress
 DNA sequence assembly and sequencing project management
 Import, edit, trim, and assemble text sequences or chromatograms from automated sequencers
 Automatic clip low-quality sequenced based on imported PHRED Quality Values
GenomBench




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Analysis and annotation of reference genomic DNA sequences
Search genomes for genes and other features by keyword, gene name, etc.; BLAT searching
Import megabase-sized genomic sequences + all associated track annotations, in an integrated, graphically rich workspace
Map sequence along the genomic backbones to determine intron-exon structure
Perform in silico workflows for full-length cDNA cloning, alternative transcript mapping, and SNP detection and annotation
BioAnnotator
 Plot physicochemical properties of DNA/protein sequences using a large selection of preloaded analysis scales
 Map protein motifs using locally stored copies of the Pfam, PROSITE, and Blocks databases
 Characterize proteolytic cleavage patterns using multiple proteases, taking account of protease cleavage efficiency
Vector NTI Database Explorer
 Search and manage sequence and other types of molecular biology data stored in Vector NTI database
The Vector NTI Database Explorer
Navigate the Vector NTI Database Explorer: Tables
 DNA/RNA Molecule Table – Stores DNA and RNA Molecules,
including constructed and designed molecules.
 Protein Molecules Table – Stores Protein Molecules.
 Enzymes Table – Stores restriction enzymes.
 Oligos Table – Stores oligonucleotides up to 1000 bases in length.
 Gel Markers Table – Stores gel markers that can be used in Vector
NTI’s simulated electrophoresis.
 Citations Table – Stores citations retrieved through the Vector NTI
PubMed Search engine, from the NCBI website or from other searches. It
provides complete bibliographic conversion features.
 BLAST Results – Stores independent of molecules in a BLAST Results
database.
 Analysis Results – Stores results from various analysis, such as PCR
analysis, PFAM analyses, etc.
Vector NTI Database Explorer: Menu, Toolbar Commands and Selections
 Menu/Toolbars – Notice the switch of the menu list when
clicking between the Subset pane and the Database object pane.
 Popular Toolbars
-- Create a new subset
-- Remove a subset without affecting the database objects.
-- Search database objects.
-- Rename a subset or database object.
 Selecting multiple database objects
☺ SHIFT + CLICK to select all objects within a range
☺ CTRL + CLICK to select non-contiguous objects in a list
☺ “Wire-frame” selection (press the mouse button somewhere outside item
names/icons and drag the selection rectangle)
Vector NTI Database Explorer: Create A New Database Subset
1. Select Menu|Table > New > Subset OR click the New
Subset button to create a new (empty) subset with a
default name, Group 1, which can be renamed.
2. Select Menu|Table > New > Subset (using Subset
Editor) to create a new subset and select its contents
in the Edit Subset dialog window.
3. To simultaneously create a new subset and include
objects in it:
> Select objects for the new subset in the Database
Objects Pane > click the New Subset button > use the
default name or enter a new name.
Exercise #1: Create Your Own Restriction Enzyme Subset
1. For routine restriction digestion and clone operation purposes,
it is beneficial to create a restriction enzyme subset that
contains only the restriction enzymes you routinely have access
to or use.
2. Select Menu|Table > Enzymes, then on the tool bar, click the
New Subset button to create a new (empty) subset with a
default name, Group 1, rename it as “my enzymes”
3. Click the Enzymes (MAIN) under the All Subsets from the left
pane to display the main enzyme database in the right pane of
the object display.
4. With the Ctrl key pressed, use mouse to select your enzymes
and then drag-drop the selections to the “my enzymes” subset.
Vector NTI Database Explorer: Edit a Database Subset
 Dismiss a subset
Select the subset > Menu|Table > Dismiss Subset, OR click the Dismiss Subset
button. This operation removes a selected subset, but DOES NOT affect the
database objects in the main database.
 Clear a subset
Select the subset > Menu|Table > Table > Clear Subset to exclude all objects from
the selected subset. The subset itself is emptied but not removed. This operation
DOES NOT affect database objects.
 Delete the content of a subset
Select the subset > Menu|Table > Delete Contents from Database to physically
delete from the database all objects of the specified subset. The objects in the subset
are PERMANENTLY DELETED from the Vector NTI database, and the subset
itself is removed.
 Rename a subset
Select the subset > Menu|Table > Rename Subset OR click the Rename button.
 OR: Click the right mouse button
All above operations can be done by clicking the right mouse button while the
desired subset is selected > then choose desire actions from the menu.
Vector NTI Database Explorer: Import Molecules
 Drag and Drop Import
In Windows Explorer, select molecule(s) from text files/or a folder containing the
files > Drag and drop the selections onto the desired subset in Vector NTI Explorer.
Exercise #2: drag and drop nm_002660.gb and nm_002660-fasta.txt into a subset from the “Vector NTI
workshop” folder on the desktop.)
 Import with choices > Select Menu|Table > Import, select one of the
following options:
1. Import Molecule From Text File – imports DNA/RNA/protein molecule data.
Accepted format: GenBank/GenPept, EMBL/SWISS-PROT, and FASTA files.
2. Import Sequence From Text File – imports a nucleotide or amino acid
sequence text file, creating a new DNA/RNA/protein molecule with the sequence.
Accepted format: ASCII format text files.
3. Import Molecules From Archive – imports objects from a Vector NTI archive.
Accepted format: Vector NTI archive .mr format.
4. Import Molecules From Directory of Text Files (molecules and oligos only)
Accepted format: GenBank (DNA/RNA), GenPept (protein) or Vector NTI’s oligo
text format (oligonucleotides).
Vector NTI Database Explorer: Export a Subset
 Export a subset into a Vector NTI Archive file
Select Menu|Table > Export > Subset into Archive to export all objects of
the specified subset to a VNTI archive > In the Write To dialog box,
indicate the directory or folder, and file name for archive storage > Click
the Save button.
 Export all subset objects into a directory of text files
(molecules and oligos only)
Select Menu|Table > Export > Subset to Directory of Text Files to export all
objects of the specified subset into a directory of text files in GenBank
(DNA/RNA molecules), GenPept (protein molecules) or Vector NTI’s oligo
text format (oligonucleotides) > In the dialog box, browse for the location
and enter the file name under which the subset is to be stored.
 Export a subset into an archive file is a great way to
backup/transfer personal Vector NTI data.
Basic Steps for Database Search
The Database Explorer allows sophisticated search by different
criteria to locate any object in the database.
1. Select a desired database table – Any searches are confined within a specific type
of database objects, one must specify a database type before the search.
2. Select filters – Menu|Database > Search OR Click the Search button > in the
Database Search Dialog Box, check the boxes for desired filters.
Basic Steps for Database Search—Continued
3. Define filters – Open the Filter Setup Dialog Box for desired filters and further
configure the filters. When multiple filters are checked, a search that satisfies all the
search criteria (an AND search) will be performed. Check ONLY the filter(s) that you
want to include into the search.
4. Start search – Inspect the final configuration of the Search Database Dialog Box >
Click Start Search button.
5. Save the search results – when the search is finished, the Insert Search Results into
Subset dialog box will appear > select an existing subset and Vector NTI will remove all
existing contents in that subset before placing the search results into it; OR Enter a new
name for the subset and all the search results will be saved to this new subset.
Vector NTI Database Maintenance
1. Database Backup
Routine backup of Vector NTI database is extremely important. It should be
performed at least once a month if not every week. Backups should be stored on both
the hard drive and a removable media, such as a CD.
– Menu|Database > Database Backup > in the Choose Backup Directory dialog box,
select an existing folder OR create a new folder to store the backup.
Note: Vector NTI Database Backups are NOT cross-platform compatible (i.e. the Vector NTI Database
on a PC cannot be restored using a VNTI Database Backup made from Vector NTI on a Macintosh,
and vice versa. For cross-platform backup/restore, users must use VNTI Archive command with each
subset (Export and Import command).
2. Database Restore
This operation restores ALL database files from a specified backup.
– Menu|Database > Database Restore > in the Choose Backup Directory dialog box,
select the directory where the last backup was stored > the database will be restored.
Warning: the restored database will overwrite all current database files.
3. Database Cleanup
This operation removes accumulated “junk” data. It may also be used to recover lost
or damaged files or tables. The cleanup should be performed on monthly basis.
– Menu|Database > Database Cleanup.
Vector NTI Database Migration Strategies
1. Moving/copying entire database from PC to PC
From Version 9.0 to Version 10
>> Copy the entire database folder in the source PC (200-500 MB) to a removable media. The
default folder name is “VNTI Database”, located on C:/ >> Move the source folder to the hard
drive of the target PC >> Open ONLY the Vector NTI Explorer on the target PC >> set the local
database by Menu|Database|Select local database >> navigate to locate the database folder >> the
Vector NTI Explorer will restart to make the newly selected database as the default database.
Note: this is the BEST strategy for both database migration and backup as it retains everything (data
and subset information).
From Version older than 9.0 – same as the strategy used for moving between PC and
MAC as described below.
2. Moving/copying entire database between PC and MAC
>> Archive each subset of each types of data from the source computer >> Import each archived
file using Vector NTI Explorer on the target computer.
Note: This strategy requires some efforts, but it ensures that all subsets will be correctly moved
between different platform or between old and new version of Vector NTI.
Vector NTI: Display Window Organization
1. In Vector NTI Explorer, from the DNA/RNA Molecules table, double click
“pACYC184” to open this molecule in the Vector NTI main module.
2. Overview of the 3-pane basic layout
 Text Pane
— displays textual info on molecule descriptions, features, comments, annotations,
and various analysis results.
 Graphic Pane
choices.
--- graphically displays the molecule, along with features and properties of your
 Sequence Pane
---displays formatted nucleotide or amino acid sequence, along with your
choices of restriction sites, motifs, ORFs, reading frames, etc.
 To change the layout of display:
 Successively click on the √ Icon from the main tool bar
 To display the inter-connection between the Graphic and Sequence panes
 Sequences can be selected either in the Sequence Pane or the Graphics Pane
 Features in the Text Pane can be located in the Sequence Pane by clicking on the Search Sequence
Button .
Vector NTI: Display Window Organization
Main Menu
Main Toolbar
Pane Selection
Toolbar
Pane Toolbar
Text Pane
Graphics Pane
Sequence Pane
Vector NTI: Display Setup (DNA/RNA)
1. To configure the overall display of a molecule, click
(Display Setup button) from
the Pane Toolbar to open the Molecule Display Setup dialog window.
2. Click different button and configure different sets of properties.
3. Click the Save To File button to save the customized display profile for future use.
Select the molecular
features to be
displayed
Configure the text
format of the
sequence to be
displayed in the
Sequence Pane
Select the restriction
enzymes whose sites
will be displayed
Load and apply the
customized display
profile to the
current molecule
Select the sequence
motif (or oligos) to be
displayed
Select and configure
the open reading
frame display
Save the customized
display profile for
future use
Vector NTI: Graphics Display Setup (DNA/RNA)
1. To configure the overall display of a molecule, click
(Graphic Display Setup
button) from the Pane toolbar to open the Graphics Display Setup dialog window.
2. Select the desired molecule feature and then modify the display style. different button
and configure different sets of properties.
3. To modify the style of a specific feature directly from the graph, mouse click to select the
feature>right click mouse button>select the feature setup>change its style in the Graphics Display
Setup dialog box
Select the
molecular features
to be modified
Turn on/off
Label display
Select desired
symbol style
Select the types
of information
to be displayed
as the Label
More selection
of symbol styles
Vector NTI: Editing the Molecule Map
The elements of a Vector NTI molecule map are divided into two categories:
1. Intrinsic features/elements (un-editable)
Derived from automated sequence calculation/analysis, such as restriction
sites, motifs, ORFs.
2. Annotated features/elements (editable)
Explicitly described in the molecule data, such as annotated
sequence/function features.
 Edit an existing feature
Double click to select the feature, then choose Menu|Edit > Feature
Properties>made desired changes in the Molecule Feature dialog box.
 Add a new feature
Select the desired sequence in Graphic or Sequence Pane, then choose
Menu|Edit >New >Add Feature to FMap (or click the Add Feature button in
the Pane Toolbar) >add description and the name for the new feature.
 Delete a feature
Select the feature, then choose Menu|Edit>Delete Feature from FMap.
Vector NTI: Fine-turning Graphics Display
The Vector NTI graphics can be edited in two different modes:
 Molecule Editing Mode (the default mode)
Allows users to modify a molecule itself, such as
adding/removing various types of features, restriction sites, as
well as changing label/symbol styles.
 Picture Editing Mode (click the Edit Picture Button
)
 Allow users to format the EXISTING labels/symbols/arrows, to
re-arrange the locations of the labels/symbols/arrows
 Allow users to add a text annotation on to the graph  click the
Add Annotation button
 enter annotation text  mousedrag the Annotation text box to any desired place.
Vector NTI: Editing sequence in the Sequence Pane
Sequence editing in the Vector NTI Sequence Pane make use of standard Clipboard
operations: Cut (delete), Copy, Paste (Insert).
 Delete sequence
Highlight the target sequence in the Sequence Pane > press the Delete key and
confirm the delete action.
 Copy sequence
Highlight the target sequence in the Sequence Pane > simultaneously press the
Control and C keys, the copied sequence is in the standard text format and can be
pasted/inserted subsequently.
 Paste (insert) a copied/cut sequence
Move the mouse cursor to the target insert point in the sequence > paste the cut or
copied sequence with the Paste button from the Panel Toolbar.
 Insert a new sequence fragment manually
Place the mouse cursor at the target insertion point, then choose Menu|Edit > New >
Insert Sequence; in the Insert Sequence dialog box, manually enter the sequence to
be inserted > click OK > when applicable, choose delete or keep of any affected
existing feature.
 Revert the insertion
Any inserted sequences can be deleted manually, OR, select Menu|File > Revert to
Saved, to restore the molecule to its unedited version.
Vector NTI: Import Molecules From NCBI GenBank Records
1. Locate the target molecule from the NCBI GenBank (recommend FireFox Internet browser).
2. Select the desired features and record display format
 FASTA: sequence + key information about the molecule
 GenBank: sequence + key information + annotations and references
3. Import the molecule into the Vector NTI in several ways:
 Direct copy and past operation
Set Send to option to Text, highlight the entire record and then simultaneously press Ctrl and C
keys to copy the selection to the Clipboard > Switch to the Vector NTI, then Menu|Edit > Open
from Clipboard > choose appropriate format and click OK to import the molecule.
 Save as a file or directly open with Vector NTI
Set Send to option to File, then either choose Save to Disk (the file will be saved in .gb format)
OR choose Open With and select Vector NTI to import the molecule
4. Batch Import multiple molecules
 From NCBI site -- Use the NCBI Clipboard feature to temporarily save multiple GenBank
molecule records (up to 500). When done, open the Vector NTI, use the Open from Clipboard
function to batch import the molecules. (more testing)
 From files contains multiple molecules, in FASTA or any GenBank format – In Vector NTI
Explorer > Create a new subset where the molecules will be imported > Open Windows
Explorer, located the molecules file(s) > Use mouse to directly drag the file(s) and drop to the
new subset in the Vector NTI Explorer, OR use the Copy-then-Paste commands.
The NCBI
Clipboard tool
can
temporarily
store up to
500 item for
later export.
Select the desired Display
Format:
FASTA -- sequence only
GenBank(full) -- sequence
plus all annotations and
references
Select the output option:
Text – for direct copy and
paste
File – save to a file or open
directly in Vector NTI
Clipboard – temporarily save
the record for later import
Vector NTI: Save the Imported Molecules
1. Imported molecules must be saved before any analysis can be performed.
2. To save a molecule, choose Menu|Save As to open the Save As dialog box, select desired
destination
 Save As File: save the molecule to a file in desired format and name for transport
purpose or to be processed by other software. NOT recommended as the saved molecule
will not present in Vector NTI database.
 Save in DNA/RNA (or Protein) Database As: save the molecule in desired subset of the
Vector NTI database.
Select the desired
destination for
the new molecule
Choose the
desired subset
to place the
new molecule.
Enter the
name of the
new molecule
Vector NTI: Import/Create New Molecules Using the Sequence Editor
1. Copy the plain sequence (ASCII format) to clipboard (ctrl+c) > in Vector NTI,
choose Menu|File > Create New Sequence, choose appropriate sequence editor to
open the New DNA/RNA (or Protein) Molecule editor dialog box.
2. Enter relevant information into the fields under each tab
 General Tab: molecule name, sequence + key information about the molecule
 Molecule Tab: basic types of the new molecule
 Sequence and Maps: click the Edit Sequence button > click Paste button to paste the
sequence from the clipboard. Customized molecule features and restriction sites can also
be entered under this tab.
 User Fields Tab: user information related to the new molecule.
 Keywords Tab: applicable gene/organism names, and your unique identifier (such as your
last name) to help you find this molecule use the Search feature in the future
Click the OK
button when
completed to
save the
molecule into
the Vector
NTI database
Vector NTI: PCR Primer Design Overview
1. To initiate PCR analysis in Vector NTI, choose Menu|Analyses
> Primer Design > select desired application mode.
2. Vector NTI provides seven PCR application modes:
 Find PCR Primers - Finds primers for a DNA selection within the
selected region.
 Amplify Selection - Defines allowed regions upstream and downstream of
the selected area for primer design.
 Amplify Features - Amplifies one or more selected features in a molecule.
 Long PCR - Designs primers for the amplification of regions that exceed
20 KB in length.
 PCR Using Existing Oligos - Searches for suitable PCR primers from
among those selected from the Vector NTI Oligo Database.
 Alignment PCR - Design PCR primers for amplifying a region of aligned
DNA molecules.
 Multiplex PCR – Designs PCR primers for amplifying several target
sequence regions in one reaction.
Vector NTI: Find PCR Primers Dialog Box
1. The Find PCR Primers Dialog Box allows users to set various parameters and
preferences for desired PCR primers and product.
2. Users can configure various parameters under each tab:
 Primers – region, length for both amplicon and primers, Tm and GC% range for
the primers, options to use defined primers or attach restriction sites to primers.
 Amplicon - %GC range, base specification near primer annealing sites.
 Structure – acceptable limits for repeats, palindromes, hairpin loops, restriction
sites.
 Pairs – Tm and GC% differences between the two primers, primer-primer
complementarity and 3’ end complementarity.
 Similarity – sequence similarity between primers and targeted sequences.
 3’ End – base specifications at 3’ end of the primers.
 Uniqueness – the uniqueness of the primers with respect to the amplicon.
 Quality – weight of each parameter on the rating of the primer quality
 Filter – molecular features to be excluded or included as potential sites for the
primers
3. Users can save the customized settings under each tab and load them in the future to
avoid repetitive configuration efforts.
Vector NTI: Find PCR Primers Dialog Box
Click each tab
to set various
parameters
and design
preferences.
Click the button to
select the desired
restriction sites to
be attached to 5’
end of primers
Save or Load
customized
parameter
settings
Click the
More>> OR
Less<< button
to see more
design options
Click the button
to select existing
primers
Click the Apply
button to accept
all settings; Click
OK to start the
primer design
process
Vector NTI: PCR Primers Analysis Results
The PCR Analysis Folder in the Text Pane contains the results of PCR analysis, organized by each
potential PCR product.
Save all PCR products
or primers on the short
cut menu with mouse
cursor over the PCR
Analysis Folder
Primer rating (typical
Max rating is 171):
ratings above 120 may
be adequate.
Sequences, differences
and other key
information of the
primers pair
Key information of
a PCR product
Save the individual
PCR product as a
molecule in Vector
NTI database on the
short cut menu with
mouse cursor over
the desired PCR
product
On the short cut menu
with mouse cursor over
the desired primer:
Analyze: opens Oligo
Analysis dialog box for
performing oligo
analysis
Add to Oligo List: for
ordering primers
Save To Database: store
the primer in the Vector
NTI database for future
use
Vector NTI: Translation Analysis
1. Translations can be performed in two ways:
 Translating in the Sequence Pane – Choose Menu|Analyses > Translation > In
Sequence Pane > select desired option.
 Translating into a New Protein Molecule – Choose Menu|File > Create New
Sequence > Using Translation Procedure > select strand option.
2. Translation options:
 Direct Strand – direct strand translation of the current selection.
 Complementary Strand – complementary strand translation of the current
selection.
 Six Frame Translation – translate both direct and complement strand with all
possible reading frames.
 Features – translate selected features.
 CDS with Splicing – translate CDS by joining the exons.
3. Setting the genetic code for translations:
The default standard genetic code may not be appropriate for some microorganisms
and organelles. To change the genetic code, select Menu|Analyses > Translation > Set
Genetic Code to open the Genetic Codes dialog box. Customized genetic codes can
also be created here.
Vector NTI: Back Translation Analysis
To launch the Back Translation dialog box from a protein molecule display window, choose
Menu|Analyses > Back Translation.
The original
protein sequence
Change the genetic
codes if necessary
The resulting
DNA sequence
from the back
translation.
Change the Codon
Usage Table if
needed
Move the slider to
change the codon
ambiguity level
Copy all/part of the
back-translated
sequence to clipboard
then open by
Menu|Edit > Open
from the Clipboard >
select Nucleotide
Sequence File (ASCII)
format
Vector NTI: Restriction Analysis – Set up the Restriction Map
Set up the Restriction Enzyme Preferences and Map before performing restriction analysis. To do
so, choose Menu|Analyses > Restriction Analyses > Restriction Sites to open the Restriction Map
Setup dialog box.
Add new REN
from the Choose
Database Enzymes
dialog box
The default list of
the restriction
enzymes
Remove any/all
default REN.
Set Terminus
Types for
desired REN
Set the maximum
and minimum
allowed sites for
desired REN
Set allowed
regions for
desired REN
Vector NTI: Multiple sequence alignment using AlignX
1. AlignX performs multiple sequence alignment using a modified Clustal W algorithm. It
incorporates the following features:
 Profile alignment: sequence + key information about the molecule
 Guide tree construction
 Secondary structure consideration
 Color-coded alignment presentation with automatic consensus calculation
 Full alignment editing capabilities
 Dot Matrix comparison of any two sequences
2. Launch AlignX in several ways:
 Direct launch from Microsoft Windows – select Start > Programs > Invitrogen > Vector NTI
Suite 10 > AlignX. Drag the selected molecules from the Vector NTI Database Explorer into the
AlignX workspace to start the alignment.
 Launch from Vector NTI Database Explorer – select the target molecules, then choose
Menu|Align > Align Selected Molecules
Use mouse or
press Ctrl+A to
select all
molecules
Choose Align or Align
Using Profile
Configure alignment
parameters if desired
Vector NTI: the AlignX Workspace
The Vector NTI AlignX Window has a four-pane layout that enables various alignment tasks.
Alignment
Similarity Plot:
normalized
representation of
sequence identity
among all
molecules at each
position.
Text Pane:
information
on the
molecules
aligned
Guide Tree
Pane:
phylogenetic
tree like
relationship
based on NJ
algorithm
Absolute
Complexity Profile
of the multiple
alignment
Editable list of
the molecules
aligned
Alignment Pane: colorcoded alignment and
consensus sequence
Absolute
Complexity
Profile of the
pairwise
alignment for the
molecule selected
in the Guide Tree
or Alignment
Pane.
Vector NTI: Sequence assembly/edit using ContigExpress
1. ContigExpress uses CAP3 to assemble and edit sequencing fragments, in
forms of text sequences or chromatograms from automated sequencers, into
contigs. It incorporates the following features:
 DNA sequence assembly and sequencing project management
 Import, edit, trim, and assemble text sequences or chromatograms from
automated sequencers with direct views of chromatograms.
 Automatic clip low-quality sequenced based on imported PHRED Quality
Values
 Improved 5’ and 3’ trimming of vector contamination
 Save and manage contigs as GenBank, EMBL or FASTA files.
2. Launch ContigExpress in several ways:
 Direct launch from Microsoft Windows –
Select Start > Programs > Invitrogen > Vector NTI Suite 10 > ContigExpress. Drag
the selected molecules from the Vector NTI Database Explorer into the AlignX
workspace to start the alignment.
 Launch from Vector NTI Database Explorer –
select molecules, then choose Menu|Assemble > ContigExpress > Assemble Selected
Molecules.
Vector NTI: ContigExpress Contig Workspace
The Vector NTI ContigExpress Window has a multi-pane layout that integrates components in
linked text, graphics, and alignment pane.
Toolbar:
Tools for
searching,
editing and
other
operations
Graphics Pane:
views of positions
of fragments
relative to a contig;
Coverage Map and
Weigh Graph of a
contig.
Text Pane:
information
on the
contigs and
fragments
Translated
sequences
Chromatogram Pane:
display chromatogram
from each fragment
Vector NTI: ContigExpress Contig Project Explorer Window
Tree Pane:
historical
relationship
between the
assemblies in
a tree form
Contig Pane:
contig and
corresponding
fragments.
Contig Display
toolbar: select from
four different
contig display.
Assembly Setup
dialog box for
setting various
parameters.
Vector NTI BioAnnotator Overview

Key Functions



Perform various physiochemical property analysis of DNA and protein sequences
Analyze secondary structural conformational parameters of protein sequences.
Perform advanced search and analysis of protein domains and functional sites.

Launching BioAnnotator
In Vector NTI Database Explorer or Vector NTI main window, with a molecule highlighted,
select Menu|Analyses > BioAnnotator > Analyze Selected Molecule.
Test Pane:
Textual
information on
sequence and
physiochemical
properties
Sequence Pane
Plot Pane:
Visual
presentation of
analyzed
physiochemical
properties
Key BioAnnotator Analyses

DNA/RNA Analyses

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Free Energy (dG), Enthalpy, and Entropy
Melting Temperature (Thermodynamic or GC Content)
GC Content (%)
Nucleic Acid Distribution (%) and Sequence Complexity

Key Protein Analyses*
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Amino acid composition
Various hydrophobicity scale, constant, indices
Various conformational parameters for secondary structural units (alpha helix, beta-sheet,
parallele and antiparallel beta strand, beta-turn, and coil)
 Hydropathicity
 Hydrophilicity scale
 Hydration potential
 Refractivity
 Polarity
 Various retention coefficient
* Nearly all protein analyses (over 50) are based on ProtScale algorithm, which allows the
computation/representation of the profile produced by any amino acid scale.

Advanced Protein Analyses (run from the Analysis Monitor)
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BLOCKS – Use the BLOCKS database to locate common sequence motifs
PFAM -- Use PFAM database to locate likely domains.
Proteolytic Cleavage – Report digestion fragments for designated cleavage reagent.
Prosite – Use the database of protein patterns and profiles to predict the function of a protein.
Vector NTI GenomeBench Overview
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Key Functions
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Retrieve data from public DAS-compliant genome severs such as UCSC, Ensembl, WormBase,
euGene, TIGR Arabidopsis.
Provides an interface for browsing/querying the genome databases, and BLAT or SSAHA
similarity searches.
Map a given sequence onto a genomic backbone using Sim4 or Spidey alignment tools.
Annotate and creat a local copy of a genomic region.

Launching BioAnnotator
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To launch GenomBench, select Start > Programs > Invitrogen > Vector NTI Suite 10 >
GenomBench, assuming a default Vector NTI Advance installation has been performed.
Feature Map Pane:
Graphic depiction
of features
Information Pane:
Display sequence,
alignment, features and text
information about the
genomic sequence displayed
in the Feature Map Pane
Final Hands-on Exercise
Epidermal Growth Factor receptor (EGFR) is
considered as one of the bio-markers for several
forms of cancer including Breast and Ovarian
cancers.
 Create a Vector NTI molecule file for one EGFR
form (Refseq Accession Number: NP_005219)
 Design PCR primers to amplify any one domain of
your choice present in EGFR protein.
Have questions or comments about this
workshop? Please contact us:
Yi-Bu Chen, Ph.D.
Bioinformatics Specialist
Norris Medical Library
University of Southern California
323-442-3309
[email protected]