SnapGene Version 4.0.0

SnapGene 4.0.0 was released on July 20, 2017.

Overview

Version 4.0 takes SnapGene to a new level of utility by supporting “collections”, which are browsable and searchable databases of DNA and protein files.

Other changes improve the responsiveness and stability of the software.

Make and Browse Sequence Collections

Store DNA and protein files in specialized folders that allow the contents to be browsed with a flexible interface. Sort the files by name, code number, or date added. Define a “Main Collection” that can be shared by a group, and create personal collections for individual projects.

Search a Collection

Choose from a wide set of options to find files with specific contents or properties.

Annotate Introns Faster

With a translated feature, convert lowercase regions to introns, or convert existing introns to lowercase.

Do a Batch Replacement

Use a collection to perform batch replacement of a specific DNA or protein sequence, feature name, primer name, or sequence author.

Define a Sequence Alias

Display an alternative name for a plasmid or other sequence.

Import Swiss-Prot Files

Open protein sequence files in Swiss-Prot format directly in SnapGene.

New Functionality

• Added support for browsable “collections” that can be used to organize and sort DNA and protein files as well as miscellaneous files.
  (Requested by dozens of customers)
• Provided the option of defining a Main Collection that is accessible with dedicated commands.
• Enabled rapid searching of collections by multiple criteria.
• Enabled batch replacement within collections of DNA and protein sequences, feature and primer names, and sequence authors.
• Added import and export options for protein sequences in Swiss-Prot format.
  (Requested by Novozymes)
• Added "Annotate Lowercase Regions as Introns" command.
  (Requested by Helena Pires)
• Added "Convert Introns to Lowercase" command.
• Added support for sequence-free placeholder files.
• Added optional “aliases” for display of alternative sequence names in Map view and in collection lists.
• Enabled SnapGene to show dynamic alerts and other targeted messages.

Enhancements

• Enhanced sequence trace windows to support Edit → Make Uppercase/Lowercase.
• Configured the Add Feature dialog so that mandatory qualifiers that have not yet been specified are shown by default.
  (Suggested by John Ticehurst & Brendan)
• Improved the GenBank and EMBL file format exporters to include primer data.
  (Requested by Novozymes)
• Allowed the preferences file to disable checking for and installing updates by setting "updates/disable=true".
  (Requested by Novozymes)
• Added a Cmd+Shift+K keyboard shortcut for "Set DNA/Protein Color”.
  (Requested by Chandler)
• Made various optimizations and textual and color enhancements.
• Added Aldevron to the list of standard authors.
• Added "Peak Height: #" information to trace viewer tooltips, and removed quality information from tooltips for failed called bases (N's).
• Added the ability to override the Flexera server address and port number encoded within a license file, to facilitate moving a Flexera server or using multiple Flexera servers on disparate networks.
• Updated and improved the Addgene plasmid importer.
• Enhanced the feature dialogs regarding qualifiers that support multiple values, to support clearing a single qualifier value by clicking the minus button.
• Enabled rapid insertion of a feature with the Insert Feature dialog by double-clicking within the list.
• Added File and Actions menus to the launch dialog on Windows, so that the researcher can create a synthetic construct or plan a cloning experiment without first opening a file.
• Enhanced manipulation dialogs so that the viewer contents are blurred before a template is specified, making it easier to read a message shown on top.
• Added the option during logging off or shutting down of saving documents, discarding changes, or canceling the logout/shutdown.
• Improved file associations and icons on Linux.
• Optimized the import of primers from a list.
• Improved reading and writing GenBank files, and prioritized use of the /label qualifier for storing feature names.
• Updated the common features database.
• Enhanced importing references from EMBL to use RG entries if no RA entries are provided.
• Added biotechrabbit MW markers.
  (Requested by Nadine Waeber)
• Added Penn State MW markers.

Fixes

• Prevented an error message from being shown twice when attempting to edit a primer by double-clicking it within a manipulation dialog.
  (Reported by Walter Bonacci)
• Fixed various issues with feature and primer tooltips, and with exporting feature and primer qualifiers to GenBank and EMBL formats.
  (Reported by Xavier Danthinne)
• Improved the rendering of arrowheads for reverse directional ORFs that wrap around the numerical origin in linear maps.
  (Reported by Max Juchheim)
• Ensured that "Linearize by PCR" is automatically checked in a manipulation dialog after replacing an enzyme-based selection with a standard selection.
  (Reported by John Murray)
• Enabled the opening of older Geneious files.
  (Reported by Sandra Malmgren Hill)
• Restored consistent opening of .exdna files created by EnzymeX.
  (Reported by Yuichiro Tsuchiya and Lennert Janssen)
• Fixed an issue that prevented "Open" links on web pages from working with SnapGene Viewer (and in some cases SnapGene) on Windows if the application was not already running.
  (Reported by Henry Chu)
• Fixed an issue where on NTFS volumes all files were falsely assumed to be readable and writable.
• Ensured comma separation of large size values when exporting features.
• Included "About SnapGene" as an entry that can appear in the list of open windows on macOS.
• Ensured that minimizing or restoring a sequence trace results in an associated Chromatogram Data dialog being hidden/restored.
• Improved the name in the Windows menu for an Align Full Sequence window.
• Corrected a cosmetic issue when using the Replace Bases dialog for a sequence trace when no replacement was specified.
• Prevented an entire sequence or trace from being deleted.
• Ensured that Edit → Paste Reverse Complement pastes the reverse complement instead of the copied text when interacting with a sequence trace.
• Enabled updates to local enzyme sets to be reflected in open manipulation dialogs.
• Enabled Edit → Undo/Redo and the associated keyboard shortcuts to work while using the Insert Codons dialog.
• Corrected a warning message about deleting the underlying sequence to specify “protein” rather than “DNA” when working with a protein sequence file.
• Corrected a command in the Edit menu to read “Delete Primers” rather than “Delete Bases” if a pair of complementary primers is selected.
• Corrected a menu command to read “Amino Acids” rather than “Bases” when working with a protein sequence file.
• Fixed an issue in which selecting one or more primers that do not result in a DNA selection, and then holding Opt while clicking Edit → Delete Primers, would inappropriately generate a request for a DNA selection.
• Ensured that "Zoom All" does not attempt to zoom windows that lack support for maximizing.
• Enabled the "Zoom" and "Enter Full Screen" commands for all windows that support full screen mode.
• Prevented the Restriction Enzymes window from allocating its own menu bar on macOS.
• Ensured that the file extension for open sequence trace files is listed in the Window and Dock menus.
• Prevented the "Set DNA Color" command from being enabled in read-only contexts such as manipulation dialogs where such changes would be lost.
• Fixed an issue where View → Toolbars → Show/Hide Toolbar could not be used to toggle the side toolbar in manipulation dialogs.
• Enabled showing/hiding and customizing a top toolbar in the New Synthetic Construct dialog.
• Prevented recent files from being cleared if SnapGene is run from the command line with an option that exits the app before the Recent Files list has loaded.
• Improved the behavior with code signing dll's and exe's on Windows.
• Improved the default folder name when exporting two or more common features.
• Improved the error message shown when attempting to register a network license from an invalid IP address.
• Corrected the font size for aligned sequence names at the lower left of Sequence view on Windows.
• Hid the scaling slider when showing an aligned sequence of a type such as FASTQ that has quality data but no trace data.
• Improved the rendering of protein feature lengths when printing Features view.
• Fixed an issue with the default Start folder name when installing on Windows.
• Ensured that menu tooltips are invisible when a parent cascading menu is hidden.
• Adjusted the Sequence Author combobox in the Description Panel to not display a clicked action text such as "Edit Sequence Author List...".
• Ensured that undoing changes to fields in the Description Panel can be achieved by invoking the Undo action once rather than twice.
• Corrected the algorithm for choosing a directory during repeated export of common features.
• Prevented the side toolbar from being compressed when a window is resized.
• Improved the automatic design of primers for Gateway fragments that are being inserted in the reverse orientation.
• Corrected the display in Sequence view of selected segments of reverse directional features with run-on translations.
• Prevented certain amino acids from being duplicated in the amino acid pull-down menu for the /transl_except qualifier in the feature dialogs.
• Improved import and export of the /transl_except qualifier from other formats such as GenBank.
• Ensured that if a mandatory qualifier remains to be specified, a different qualifier can be edited within the feature dialogs.
• Improved the display of pliancy when mousing over the sequence name in a linear map.
• Fixed an issue with the file icon and path when right clicking the title bar for a sequence trace on macOS.
• Prevented an empty ruler from appearing in Sequence view of a cloning dialog when no template is loaded.
• Ensured that DNA colors for top and bottom strands are exchanged when inserting a fragment in the reverse orientation.
• Fixed various issues with viewing long sequence traces.
• Made various stability improvements.
• Prevented full sequence /source features from being exported when using the EMBL format to save or export DNA sequences.
• Ensured that *'s in protein files can be imported.
• Fixed an issue with writing the last base # per line when exporting DNA files to the EMBL format.
• Ensured that the Browse Common Features and Insert Feature dialogs list the correct feature subset when the dialog is opened repeatedly.