Home » Release Notes » 3.3.0

Changes in version 3.3 (Dec 21, 2016)

New Functionality

  • Added an “Insert Codons” dialog.
  • Added an “Insert Restriction Sites” dialog.
  • Added an “Insert Feature” dialog.
    (Requested by Rolf Hansen, Ron Godiska)
  • Added an “Insert Reverse Translation” dialog.
  • Added a new interface for designing a synthetic DNA construct.
  • Provided the option of browsing common features by type.
  • Provided the option of defining features as “Favorites”.
  • Added support for embedding external files in a SnapGene file.
    (Requested by Teresa Grider, Alan Howe)
  • Enabled batch conversion between file formats.
  • Enabled import from NCBI using gene ID's.
    (Requested by Barbara Baker)
  • Added an importer for Clone Manager .cx5 files.
    (Requested by Elaine Shapland)
  • Added an importer for Geneious DNA and protein .geneious sequence files.
    (Requested by Alex Triassi)
  • Added a "Cut" button to the top toolbar.
  • Added GeneDireX MW markers.
    (Requested by Kaoru Nakasone)
  • Added NIPPON GENE MW markers.
    (Requested by Kazuki Motomura)
  • Added VWR Peqlab MW markers.
    (Requested by Florian Sonntag)
  • Added Carl Roth MW markers.
    (Requested by Steffen Helbich)
  • Provided a control for vertically scaling aligned trace data.
  • Enhanced the DNA calculations window to display the copy number.
    (Requested by YC)
  • Updated TA TOPO vectors to include terminal phosphates.


  • Added a "Select Recognition Sequence" command to the enzyme context menus.
  • Dramatically sped up searching feature descriptions in Features view.
  • Enhanced import from Addgene to include PubMed references.
  • Provided Undo support for adding and removing enzymes from the chosen set.
  • Added feature and primer context menus when using action dialogs.
  • Provided robust high-DPI support on Windows.
  • Added /function data to feature tooltips.
    (Requested by Xavier Danthinne)
  • Added a 10-bp minimum ORF length menu option to the Translation Options and Preferences dialogs.
    (Requested by Jialin)
  • Added a message in the Simulate Agarose Gel dialog clarifying when enzymes cannot be used because they cut the template too many times.
    (Requested by Pieter deJong)
  • Reduced margins and improved usability of various manipulation dialogs on smaller screens.
    (Suggested by Paul Jaschke)
  • Turned off the default setting of showing translations when viewing common features.
  • Removed the long discontinued TliI from the enzyme database.
  • Added a button for restoring the default properties of common features.
  • Ensured that all display options are now maintained when switching between features in the Browse Common Features dialog.
  • Provided keyboard shortcuts in button tooltips in the top toolbar, launch dialog, and the toggle 3-letter codes button in the Map & Sequence Options dialog.
  • Improved sorting by primer Tm.
  • Switched from "kb" to "bp for the new "XLarge DNA Ladder RT" MW marker from GeneDireX.
  • Swapped order of Add/Remove buttons when editing feature qualifiers.
  • Unified toolbars in all dialogs on macOS.
  • Improved the look and feel of draggable splitters.
  • Made various textual, color, icon, alignment and other enhancements.


  • Ensured that if a window is minimized, it will be shown after clicking the associated menu command.
    (Reported by Tracy Wilson)
  • Fixed an issue where features were sometimes unnecessarily omitted from maps.
    (Reported by Tim Rand)
  • Improved the accuracy of band patterns on agarose gels after zooming.
    (Reported by Benjamin Spreng)
  • Improved stability when using the Simulate Agarose Gel dialog.
    (Reported by Joseph Sheehan)
  • Fixed an issue that caused SnapGene to hang when opening a file with a “renumber base history” operation while using the Japanese interface setting.
    (Reported by Tomomi Sato)
  • Improved the decoding of dates from 2016 and later from Vector NTI databases.
    (Reported by William Widner)
  • Improved feature import from Vector NTI protein sequences.
    (Reported by William Widner)
  • Fixed an issue with opening some MacVector .nucl files.
    (Reported by Roei Mazor)
  • Improved the display of trace data for aligned sequences when viewed on a high-DPI display using Windows.
    (Reported by William Law)
  • Removed sources of confusion when interacting with ancestral features in History view.
    (Reported by Michael Nielsen)
  • Fixed an issue with updating the position of feature cleavage arrows when performing a large insertion or replacement upstream.
    (Reported by Tore Dehli)
  • Ensured robust primer design in various contexts where compatible overhangs must be created.
    (Reported by Wei Guo)
  • Enhanced the import of oligos from Vector NTI database and oligo archives.
    (Requested by Dominique Aubert Skovlund)
  • Improved the consistency of importing full sequences from Addgene.
    (Reported by ChangHee Lee)
  • Fixed an issue where copying and pasting portions of aligned sequences could transfer invalid feature data.
    (Reported by Lianna)
  • Ensured a robust response when opening or pasting FASTA-encoded protein sequences.
    (Reported by Steven Erickson)
  • Tweaked the wording when using Cut, Delete Amino Acids, or Insert Amino Acids in SnapGene Viewer, where the resulting dialog referred to bases instead of amino acids.
  • Improved the painting of full sequence colored ranges or N-stretches in circular maps.
  • Ensured the translation of "None selected" to Japanese in various contexts.
  • Fixed an issue where if you cleared the sequence in the New, Insert, and Replace Bases/Amino Acids dialogs, the length was not reported correctly.
  • Ensured the correct font size for error message in import dialogs on Windows.
  • Ensured proper resetting of controls in the “Choose Alternative Codons” dialog after resetting the codon usage table to "None".
  • Fixed an issue where specifying "Met" in insertions controls in the Add/Edit/Duplicate Primer dialogs would result in "ATG" being listed twice in the list of codons that can be inserted.
  • Corrected the message that appears after clicking the disabled toggle 3-letter codes button when no sequence is loaded.
  • Ensured that the subsidiary controls in the Reverse Translate dialog are disabled when appropriate.
  • Fixed an issue where choosing a custom vector when using the TA, GC, or Gateway cloning dialogs did not update the Product tab.
  • Ensured that keyboard shortcuts for Undo and Redo trigger a result even if an editable pull-down menu has focus.
  • Improved the stability of circular map sizes as the window is resized.
  • Fixed a comment for BsoBI in the Restriction Enzymes dialog.
  • Ensured that it is possible to edit the directionality of multiple translated features at once using Edit DNA Features.
  • Updated the names of various enzyme suppliers and standard sequence authors.
  • Fixed an issue where dropping a file on the References pane in the Description panel should not have any effect.
  • Enhanced stability when changing the font size or triggering other keyboard shortcuts when no document is loaded in a manipulation dialog.
  • Fixed an issue where the "show features on line" button would appear in a manipulation dialog after switching away from and then back to Map view.
  • Ensured that tooltips for bottom strand ORFs show MW values.
  • Ensured that the name for files opened from web links do not use “%” encoded symbols.
  • Ensured that the "Detect Common Features" checkbox is always visible when using the "New DNA File" and "Insert/Replace Bases" dialogs.
  • Improved stability when Paste or other keyboard shortcuts were quickly tapped multiple times before the Insert/Replace Bases dialog could be shown.
  • Provided consistent use of bold font for disclosable labels in the Letter Codes dialog.
  • Prevented the display of irrelevant messages when clicking disabled buttons in the side toolbar of an empty manipulation dialog.
  • Improved the rendering of pliancy for enzymes, features, and primer names in circular and linear maps.
  • Added missing HTC and ENV (high-throughput cDNA and environmental sampling) Natural DNA sequence class options.
  • Fixed an issue that resulted in the right side of tooltips being clipped slightly.
  • Enhanced anonymous statistics to identify macOS 10.12 as "Sierra”.
  • Prevented the use of invalid characters in filenames on Linux.
  • Improved the disk image background on macOS 10.11 and later.
  • Fixed a potential hang when formatting floating point numbers for display.
  • Improved the formatting of negative floating point numbers.
  • Prevented a potential issue with invalid network time stamps.
  • Improved the translation numbering of multi-segment reverse directional features when using the Make Protein command.
  • Closed a loophole that allowed feature translation options to be edited in read-only contexts (manipulation dialogs) by using the Sequence view minimap.
  • Ensured that "Reverse Translate" using degenerate codons works for amino acids with only one codon (e.g., M = ATG).
  • Fixed an issue where TA cloning could fail when using a non-TOPO vector and phosphate groups on either the vector or insert.
  • Corrected a rare glitch where feature names in linear maps could sometimes be drawn on top of each other.
  • Improved stability when closing documents.
  • Improved stability when opening recent documents from the launch dialog.
  • Fixed an issue that prevented hiding the launch dialog on macOS using File → Close or the Cmd+W keyboard shortcut.
  • Improved stability when generating products in action dialogs.
  • Fixed an issue with macOS system menus that could cause instability or erroneous messages.
  • Prevented a rare stability issue when using the Simulate Agarose Gel dialog when a template used for PCR is modified outside the dialog.
  • Prevented a crash with Insert Bases when the session also has embedded files and thread deadlocking UI.
  • Enhanced the flexibility of opening files on macOS and Linux.
  • Prevented a crash in case an embedded trace fails to load.
  • Improved stability when quitting the application.
  • Various other stability improvements.