SnapGene Version 3.3.0

SnapGene 3.3.0 was released on December 20, 2016.

Overview

Version 3.3 provides new synthetic biology tools, as well as enhanced options for file conversion and embedding.

The software has been updated to improve performance with newer operating systems and with high-DPI monitors for Windows. SnapGene 3.3 requires macOS 10.8, or Windows 7 or later.

Insert Sequence Elements

Use dedicated commands to insert features, restriction sites, codons, or reverse translations.

Design a Synthetic Construct

Assemble a DNA construct by inserting sequence elements with the New Synthetic Construct interface.

Define Favorite Features

Designate standard or custom features as “Favorites” that can be accessed quickly from a special list.

Embed External Files

Organize your data by embedding image or document files into a SnapGene file.

Batch Convert Files

Convert an entire folder of files to or from SnapGene format in a single step.

Import Geneious Files

Open DNA and protein sequence files in .geneious format directly in SnapGene.

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.

Enhancements

• 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.

Fixes

• 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.