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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.
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Fixed major cloning defects including usability and functionality. Added support for Modifying termini ends cut by enzymes (a.ka. Bio Chemical Operations)
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Ability to select multiple fragments to be deleted from the Fragment List
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Ability to Copy with Reverse Complementary Sequences
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Ability to Revert to Last Saved Molecule
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Ability to Copy / Paste Sequence with Features in view context menu in Molecule and Sequence
Editors.
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Primer Design Analysis products sorted by delta G
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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 )
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
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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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
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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 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

Update with new NCBI Blast url

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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

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

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
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.
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
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
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.
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.

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