Home » Release Notes » 4.2.0

Changes in version 4.2 (Jul 9, 2018)

    Note: SnapGene 4.2 requires macOS 10.10 or later.

New Functionality

  • Added multiple alignment tools for DNA and protein sequences.
    (Requested by hundreds of customers)
  • Implemented tabbed window support for macOS.
    (Requested by Kasey and others)
  • Enabled import of a database in CSV format into a collection.
    (Requested by James Burchfield)
  • Enabled display in Sequence view of any of the six reading frames.
    (Requested by Assunta Diodato, Matthias Goerlach, Paul Shapiro, and others)
  • Added file exchange tools for the LabArchives ELN.
  • Allowed sequence traces to be exported to FASTA and plain text formats.
  • Added Biotium MW markers.
    (Requested by Hussein Abkallo)
  • Added "φ29 – HindIII" MW Marker.
    (Requested by Manuel Miras Marín)
  • Added "λ DNA – EcoT14I" MW Marker.
    (Requested by Nori)
  • Added Enzynomics MW markers.
    (Requested by the Department of Parasitology and Tropical Medicine)
  • Restored original "1 Kb Plus DNA Ladder" from Thermo Fisher (Invitrogen).
    (Requested by Martin Schmidt, Aminu Jahun, Chris McDermott-Roe and Shih-wei Chen)
  • Facilitated unattended installations by adding support for accepting the EULA and registering and unregistering via the command line interface.

Enhancements

  • Improved the placement of features in Map view so that certain types of related features are in the same row.
  • Made the selection behavior more consistent and predictable in Map view, especially in circular maps.
    (Requested by Thomas Seine and Elisabeth)
  • Increased the number of allowed fragments to ten when inserting or assembling.
    (Requested by Álvaro Muñoz-López)
  • Added the "Set Translation Numbering..." command to relevant context menus.
    (Requested by Karl Brune)
  • Enhanced the mouse indicator to indicate the offset within the selection when mousing over DNA bases in Sequence view.
    (Requested by Steven Erickson)
  • Improved the drag selection behavior in circular maps.
    (Requested by Elisabeth)
  • Improved the Find tool to show the closest match to the currently displayed portion of the sequence instead of the first match in the entire sequence.
    (Requested by Adrian Ross)
  • Made extensive speedups and other optimizations.
  • Enabled the NCBI importer to accept UniProt accession numbers.
  • Moved options related to files to a separate tab in the Preferences dialog, and added new options for working with files.
  • Added the option to hide the Order button, and added a "How Ordering Works" command.
  • Added a "Note About Tm Values" command that explains how Tm values are calculated.
  • Enhanced the "Format Tips" window to explain use of the COMPLEMENT operator when importing from NCBI.
  • Improved inserting codons and other content into a primer sequence by placing the cursor as one would intuitively expect.
  • Improved the default view tab shown when using "New File from Selection."
  • Migrated "Add Custom Codon Usage Table" to a dedicated button to improve discoverability.
  • Added "Choose Alternative Codons..." to the translated feature context menus.
  • Enhanced the menus in the top toolbar to provide commands relevant to collections, and added "Open File" to the Open menu.
  • Streamlined the controls in Preferences for specifying if 1- or 3-letter codes should be shown by default, by offering to mirror changes for DNA and protein sequences.
  • Added a link to "Preferences" to the launch dialog on Windows.
  • Updated the Restriction Enzymes and Common Features databases.
  • Updated the embedded vector sets for Gateway cloning and TA and GC cloning.
  • Made various color, textual, visual alignment and rendering enhancements.

Fixes

  • Ensured that "Find protein sequence" will return matches to feature translations that span multiple features.
    (Requested by John Leonard, Patrick McGrath, and Omar Bazirgan)
  • Improved the display of selected amino acids at the ends of rows in Sequence view.
    (Reported by Dan Strongin)
  • Fixed an issue with displaying feature translations when viewing primer binding sites at or near the numerical origin.
    (Reported by Lagnajeet Pradhan)
  • Enabled use of the command line interface on Linux without an X server.
    (Requested by Novozymes)
  • Improved stability when using SnapGene on Linux via VNC.
    (Reported by Tom Chappell)
  • Fixed an issue with highlighting matches and showing selections in sequence traces.
    (Reported by Moin)
  • Ensured that the "DNA Calculations" window always shows information about the active selection.
    (Reported by Scott James)
  • Ensured consistent letter spacing in Sequence view on Windows when using multiple screens.
    (Reported by Gian Mario Dore)
  • Preserved the file location in the folder hierarchy when renaming a file in a collection on Windows.
    (Reported by Carles Alvarez )
  • Preserved the original numbering of protein sequences when using "New File from Selection".
    (Reported by Karl Brune)
  • Fixed an issue with saving a file into the proper collection folder.
    (Reported by Carles Alvarez)
  • Fixed an issue with using files stored on an SMB network share via the Gnome Virtual File System (GVFS) protocol on Linux.
    (Reported by Kai Zhou)
  • Corrected a stability issue when renaming folders in collections on macOS.
    (Reported by Jorge)
  • Fixed an issue with embedding and resurrecting ancestors to protein sequences, and with undoing protein sequence modifications.
    (Reported by Karl Brune)
  • Ensured that files saved to collections always appear in Folder and List views.
    (Reported by Carles Alvarez)
  • Sped up addition, removal, and editing of custom common features on Windows.
    (Reported by Wulf Dirk)
  • Improved the unified toolbar appearance on macOS High Sierra.
  • Provided real-time feedback so that customizing the top toolbar immediately updates all toolbars to show the new options.
  • Ensured that right clicking does not modify the selection in a list in the Restriction Enzymes and Simulate Agarose Gel dialogs.
  • Enhanced History view so that if the display is limited to one level, history colors are shown for the last logged ancestor and operation.
  • Improved the display of features in aligned sequences that do not exactly match the reference sequence.
  • Improved decoding of the comment line from FASTA files.
  • Improved the rendering of features.
  • Improved the selection behavior in lists.
  • Fixed an issue where the second segment in a multi-segment feature was selected automatically when using the Edit Feature command.
  • Improved the decoding of non-UTF-8-encoded GenBank files that contain Greek symbols and other characters outside the normal alphabet.
  • Ensured that file dialogs persist appropriately on macOS.
  • Disabled the "Export DNA" command in the Simulate Agarose Gel dialog and other dialogs where it was nonfunctional.
  • Improved the display of a primer description when space is limited and the primer has multiple binding sites.
  • Improved the rendering of overlapping selections and yellow "Find" highlighting in Sequence view.
  • Improved the reliability of detecting the topology in some GenBank files.
  • Added logic to preserve the creation date from GenBank files.
  • Simplified the oligo name controls in the Anneal Oligos dialog.
  • Added licensing information to the Linux .deb package.
  • Fixed an issue with included plasmids with single quotes in their names in the Linux .rpm package.
  • Improved the import of primers from FASTA-formatted lists that are RTF encoded or compressed.
  • Configured tooltips in protein sequences to persist rather than disappearing after a brief delay.
  • Ensured that the source menu in a cloning dialog will list the active template file from a collection even if the collection is closed.
  • Fixed a bug where source menus might not always select recently browsed files with very long names.
  • Ensured that clicking Escape always hides the Find controls when viewing a sequence trace.
  • Ensured that if the clipboard contains a valid protein sequence but lacks A's, C's, G's and T's, the protein window will still allow pasting.
  • Prevented the "Import NCBI Sequences" command from hanging if no terminator symbol (//) is included at the end of the downloaded content.
  • Ensured that exact searches for queries that include U will produce correct matches on the bottom strand of DNA sequences.
  • Ensured that "Undo" will revert the modification date shown in the Description panel.
  • Fixed an issue with ordering an edited but unsaved DNA sequence from VectorBuilder.
  • Corrected links from the interface to open the relevant tab in Preferences.
  • Fixed an issue where after clearing the Sequence Author, the previous value returned unexpectedly when modifying another field in the Description Panel.
  • Improved the algorithms for displaying, updating, and copying cleavage arrows that are located at an end of a feature.
  • Improved the display of feature codon selections in Sequence view.
  • Fixed the listing in the Window menu of open collections with selected files.
  • Improved the reliability of keyboard shortcuts for commands in cascading menus on macOS.
  • Provided automatic selection of the "From" value in "Edit → Select Range" when no selection is present.
  • Improved the conversion of UniProt sequences.
  • Prevented the application from hanging when switching from a placeholder file to a non-empty sequence in a collection.
  • Disabled "View → Edit Map Labels" when no sequence is being viewed.
  • Improved batch conversion of files.
  • Improved the identification of CPU and related information on Linux.
  • Increased stability when exporting a selection.
  • Fixed a stability issue with opening compressed sequence trace files.
  • Fixed an issue with saving sequence traces using the ZTR1, ZTR2, and ZTR3 file formats.