Release Notes for Vector NTI Express Designer Version 1.1.0
What’s New and Improved in Version 1.1.0
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 1.1.0
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