Release Notes for Vector NTI Express Version 1.6.0
What’s New and Improved in Version 1.6.0
AlignX
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This release comes with a completely revamped version of the multiple sequence alignment tool,
AlignX.
A single algorithm is now used for alignment using the latest release of ClustalW v2.1 multiple
sequence alignment algorithm
Cleaner layout with improved analysis plots and phylogenetic tree rendering
Expandable panels for analysis plots, phylogenetic tree and alignment sequence panes
More responsive sequence alignment pane with support for colored residue properties
Hovering on nucleotides display tooltips show similarity and identity positions with nucleotide
location on the original sequence
Added support for updating alignment properties such as residue fraction and automatic consensus
recalculation that react with these property changes
Features copying of analysis plots, phylogenetic tree and alignment sequence view to clip board
Supports printing of plots, tree and alignment sequences
Support for searching nucleotide sequences in the alignment
Alignment can now be edited by shifting bases forwards and backwards
Sequences can now be copied over to clipboard or sent for blast search, contig assembly, or simply
saving them as molecules
You can now remove sequences for alignment and have the tool recalculate the consensus
Support for saving to the database has been removed but can be saved to a more structured data file for
better portability
User will be able to open the existing project saved in database from previous version, fragments will
be displayed. User shall execute with latest ClustalW v2.1 for alignment.
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What’s New and Improved in Version 1.5.0
Mac Installers
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The Mac version of Vector NTI Express is repackaged and bundled with JRE 1.8 to support Yosemite
Mac OSx. This version’s installer can only be installed on Lion Mac OSx or higher versions Mac OSx
3D Molecule Viewer (Mac OSx only)
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The 3D molecule viewer is launched from multiple independent windows compared to 1 embedded
window in previous releases.
Fixes to Known Issues
Issue: Application is unable to launch in Mac with java 8/jre 1.8.
Resolution: Bundled JRE 1.8 with the Mac application installer
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What’s New and Improved in Version 1.4.0
Clone2Seq
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New toolbar with zoom in / zoom out functionalities in Clone2Seq feature. In addition, users can
toggle linear / circular view of their molecules in the graphics pane.
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Added Restriction Analysis tool in Clone2Seq feature where user can run a separate restriction analysis
on each editor. This improvement allows users to configure which restriction binding sites to choose
in individual molecules.
Fixed major cloning defects including usability and functionality. Added support for Modifying
termini ends cut by enzymes (a.ka. Bio Chemical Operations)
Ability to select multiple fragments to be deleted from the Fragment List
Molecule Editor
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Ability to Copy with Reverse Complementary Sequences
Ability to Revert to Last Saved Molecule
Ability to Copy / Paste Sequence with Features in view context menu in Molecule and Sequence
Editors.
Primer Design Analysis
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Primer Design Analysis products sorted by delta G
Search
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Ability to search molecule by Name in the “Browse Molecule dialogue” for various cloning tools (
Clone2Seq, TOPO, Gateway, Part Assembler, GeneArt )
Fixes to Known Issues
Issue: Incorrect Antisense primer sequence is saved when saving Primer Design Analysis Product as new
molecule when there is a 5’ terminus attachment
Resolution:
Issue: Missing 5’ terminus attachment when Primers are sent to ordering cart
Resolution:
Issue: Contig Express – Misalignment in the sequences and chromatogram after performing assembly
Resolution:
Issue: Clone2Seq - Persisting the color (Red & Blue) in Fragment list for fragments that are opened in
Clone2Seq Editors
Resolution: The colors are now properly persisted as expected when saving a project.
Issue: Clone2Seq – Unable to clone a blunt end construct
Resolution: Blunt ends resulting from blunt ended Restriction sites can now be cloned together.
Issue: Clone2Seq – Features shown in the constructed molecule are shifted by a few bases
Resolution: Fixed problem with feature shifting.
Issue: Vector Advance Data Migration – Software crashes after clicking Configuration List in Restriction
Analysis tool after migrating Restriction Sites from Vector Advance database that do not have the
restriction type property
Resolution:
Issue: Web Analysis related to NCBI – Some of the Web analysis are not working or not pointing to the
correct program / database
Resolution: Remove Web analysis that are no longer working and redirect the NCBI related web analysis
to the correct program / database
Known Issues in Version 1.4.0
Issue: Molecule Editor (Display issue) – The display of the molecule position in the properties pane for the
constructed molecule created by Clone2Seq feature will be offset by the number of bases set in the
BioChemical.
Workaround: N/A
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Release Notes for Vector NTI Express Version 1.3.0
What’s New and Improved in Version 1.3.0
Restriction Analysis Tool
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New columns in Database Explorer to describe Restriction Enzymes: cuts after, end type, overhang,
suppliers
New field “Suppliers” for Restriction Enzymes, both in Database Explorer and Enzyme Properties
Dialog
Ability to edit “Suppliers” information through Enzyme Properties for Restriction Enzymes
The Restriction Analysis Tool interface has been redesigned to allow more intuitive selection for
filtering analysis by number of sites. Now restriction site search can be filtered by searching for single,
double, > 2 number of sites or can be specified as ranges
New feature for Restriction Analysis Search: User can provide parameters for searching sites within or
outside a particular region, and the analysis will return the appropriate results
Configuration and selection of enzymes to search for in the Restriction Analysis Tool can now be
filtered by type of enzyme (restriction enzyme or methylase), end type and supplier
Bairoch files are now supported for enzyme imports
Hovering on restriction sites in Molecule Editor now shows a display of the recognition string and the
overhangs of the site
Database Explorer
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Database Explorer is now able to persist visible columns state
Database Explorer is now able to show all information on data migrated from Vector NTI Advance
Imports now support rename, overwrite, skip, rename all, skip all, overwrite all options
Blast Search Tool
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Update with new NCBI Blast url
Data Migration
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Migration of User Defined Fields from Vector NTI Advance
Migration of Parent-descendant relationship from Vector NTI Advance
Migration of PCR, Sim4 and Spidey Analysis results from Vector NTI Advance
Migration of DNA/RNA and Protein molecules generated by Splicing
Create a backup for the current state of Vector Express and Vector NTI Advance databases before
migration starts
Destination Vector Express Database will be rolled back when migration is cancelled
Application Installation
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The Windows version of Vector NTI Express Personal Edition is introduced where single-user
installation is now available
The Windows version installer is repackaged where the un-installation process will not remove the
user database
The configuration of the application is repackaged to provide a better support for multi-user
environment
Note: Vector NTI Express Personal Edition is supported in Windows 7 and Window 8 platform
Standalone Migration Tool Installer
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The Mac version of Vector NTI Migration Tool is repackaged as OS X App Bundle. This will
introduce more Mac-friendly installation process (simple drag & drop app to the desired location) and
remove the administrative privileges requirement for single-user installation
Fixes to Known Issues
Issue: Data migration of molecules with no Author name
Resolution: For molecules with no Author name, the name would be set as ‘UNKNOWN’
Issue: Data migration of molecules and subset with spaces in their names
Resolution: The space in the name of subsets and molecules is now read and saved as it is. In previous
versions, the space was getting replaced with a “\”
Issue: Data migration will create a blank and invalid Vector NTI Express database at default database
location when started before Vector NTI Express is started
Resolution: Data migration won’t create a blank and invalid Vector NTI Express database when started.
Issue: Data Migration will crash when “Start Migration” and “Cancel” clicked repeatedly.
Resolution: Data migration will not crash when “Start Migration” and “Cancel” clicked repeatedly
Issue: Unable to import files from because the internal name is the same on multiple molecules . .
Resolution: Internal name being checked during importing, option to allow user to rename file or overwrite
existing data in the Database Explorer.
Issue: Unable to rename data in Database Explorer
Resolution: User will be able to rename data with ‘UNKNOWN’Author name. After renaming, the Author
name will be replaced with user registered name.
Known Issues in Version 1.3.0
Issue: Migrated analysis results will be displayed as “Foreign” under Local/Foreign column
Workaround: N/A
Issue: When hovering over Methylase enzymes (subset of 6 Methylase Enzymes) that cuts sequences
before recognition site, the “red” line indicating the cut sites are 1 base off. However, the indicated
sequences are correct
Workaround: N/A
Issue: Author Name will not be displayed in Molecule Editor properties pane when the migrated data
Author information are in the following conditions:
- Original Author name exists while Author name does not exists in the file
- Both Original Author and Author do not exist in the file
Workaround: N/A
Release Notes for Vector NTI Express Version 1.2.1
Fixes to Known Issues
Issue: Contig Express – Occasionally, contig with chromatogram is truncated at both ends of the page
width after printing alignment with chromatogram.
Resolution: User can print contig alignment with chromatogram without truncation at both ends of page
width
Issue: Contig Express – Printing alignment with chromatogram is slow when printing is performed in Mac
OSX.
Resolution: Performance of printing alignment with chromatogram is tuned
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Release Notes for Vector NTI Express Version 1.2.0
What’s New and Improved in Version 1.2.0
Contig Express
ContigExpress is a program for assembling and editing sequencing fragments, either in the form of text
sequences or chromatograms from automated sequencers, into longer contiguous sequences or “contigs.”
ContigExpress uses CAP3 to drive the assembly process. This widely-used sequence assembly program can
use quality value scores (QVs) in ends trimming, contig construction and consensus calculation. It also
produces excellent results when QVs are unavailable. It is capable of using forward-reverse constraints to
evaluate contigs, a feature that helps in accurate placement of repetitive sequence fragments. It can also
identify and discard chimeric sequencing reads that frequently result from lane tracking errors. One of the
major strengths of CAP3 is its consensus generation algorithm based on weighted sum of QVs.
ContigExpress analysis can be saved as a ContigExpress Project, which contains the fragments, their
assemblies, and assembly options. In ContigExpress, fragments can be edited directly, with the
chromatograms in full view. Changes are tracked and a history is maintained. The contigs generated can be
saved to theVector NTI® Express database.
Fixes to Known Issues
Issue: Display Profile - Feature Label that is edited in the Graphic edit mode will revert to the original label
display when the molecule is opened as a Molecule Document file.
Resolution: User can edit feature label in Graphic edit mode and the label can be saved and displayed
when the molecule is opened as a Molecule Document file.
Known Issues in Version 1.2.0
Issue: After doing multiple editing on the sequence, the color indication shows incorrect combinations for
matching sequences.
Workaround: Include a patch in future
Issue: Application can support saving a Contig Assembly Project with up to approximately 400 without
chromatogram fragments with 42 contigs (Each fragment size is approximately 1000bp). Saving large
Contig Assembly Project will cause out of memory issue.
Workaround: User can choose to discard Chromatogram when importing fragments into Contig Project to
avoid Out of memory issue.
Issue: Application can support running ORF for approximately 3 times for large Contig Assembly Project
with approximately 200 fragments with 20 contigs. There is out of memory issue upon running a few times
of ORF in a large contig.
Workaround: Include a patch in future
Issue: Fragments are not aligned properly when a CEP file that was previously edited by user (at the
sequence level) is imported.
Workaround: Include a patch in future
Issue: Performance - Application takes several minutes to print aligned Chromatogram to PDF in Mac OS.
Workaround: Include a patch in future
Issue: Software does not update the database when attempting to re-save an imported VA contig project
that contain contigs in forward direction
Workaround: User can choose “Open” instead of “Import” to open the Vector Advance .cep project then
do a 'Save” after editing and subsequently the save to database will work
Issue: Fragment ends trimming - trimming does not take in edited fragment sequence
Workaround: Include a patch in future