SnapGene Version 8.0.0

Overview

SnapGene 8.0 brings a fresh look and feel to the main data viewers, with new capabilities for bulk annotation and data manipulation, and new ways to edit alignments to a reference sequence.

Bulk annotate your plasmids with features and primers

Quickly detect common features and add primers from a list onto multiple sequences selected in the Project folder panel, change sequence attributes like methylation and topology and easily perform alignments and gel simulations on selected sequences.

Modern, streamlined Map, Sequence, Features and Primers views

Refreshed Map, Sequence, Features and Primers views are restructured and simplified to highlight key data and capabilities, with flexible filtering and sorting added to Features and Primers tables.

Edit Alignments to a Reference DNA Sequence

You can now validate your sequences with confidence by editing the gap positions in your Sanger traces and virtual constructs when using Align to a Reference DNA Sequence.

Enhancements to File and Folder Interactions

Data management is streamlined with improved file selection in the folder panel and new visualization and manipulation of unsaved files.

Detailed Changes

• Enhanced annotating and converting multiple files in Projects
  • Import features or detect common features in multiple DNA files
  • Import primers from a list or SnapGene, VNTI or Clone Manager files onto multiple sequences
  • Circularize, linearize, or flip multiple nucleotide files
  • Change file attributes of multiple sequences including methylation, topology, and strandedness 
  • Choose enzymes to be shown for multiple DNA files 
  • Edit DNA or RNA ends for multiple sequences
  • Make DNA, RNA, or Protein for multiple sequences
• Enhanced file management capabilities in Projects
  • Added ability to select folders and added indication of partial folder selections
  • Quickly clear the entire selection or deselect files by type
  • Deselect files for other types by Opt/Alt clicking the X right of the file count for a given file type
  • Added help link
  • The file / folder selection is now cleared when closing the last tab in the project window.
• Improved visualization and manipulation of unsaved changes
  • A yellow dot is shown next to files in the folder panel and in the tab. 
  • An alert is shown at the top of the project folder tree. 
  • Added options to Save All, Discard All or Select Unsaved Files in the project
• Modernized Map and Sequence Views
  • Moved tabs to the top and the selection bar to the bottom
  • Move sequence view minimap to bottom of the view
  • Moved the chosen enzyme set indicator to the selection bar
  • Replaced the Zoom button at the bottom left (which can still be accessed view the View menu) with a Find button to toggle the search controls and added support to search while viewing a ssRNA or ssDNA structure.
  • Replaced the “Description Panel” checkbox at the bottom with an “Info” button at the top.
  • Replaced the “Language” button at the top left with a “Settings” button.
  • Streamlined the side toolbar by moving less commonly used actions to side menus and/or a new Display button at the top right. Consistent predictable icons now shown regardless of view option settings.
  • Updated the look and feel of controls at the top right of history view and the message that is shown if no history is present.
  • Added a green checkmark icon at the top right to indicate if a sequence is “Confirmed Experimentally” 
  • Updated, added, and modernized many tooltips which now show without a delay
  • Modernized and now dismissable alerts have been moved from the top to the bottom right.
  • Alerts for content (such as enzymes, features, or primers) that could not be shown now include a link to a comprehensive list and information on what the user can do to see more of the desired content.
• Modernized Features and Primers views
  • Modern look and feel
  • Allow expanding and collapsing individual features and primers
  • Moved find field to the top which now filters the table
  • Find matches now highlighted in table
  • Added ability to sort columns in reverse direction
  • Added ability to quickly change the color of annotations using a color picker
  • Added checkboxes to indicate and modify the selection
  • Added a tooltip for alternative start codons
• Added support for shifting bases across gaps when viewing an alignment to a reference sequence. Shift bases across gaps by a single base or completely (by holding Alt or Opt) using the arrow keys.
• Enabled creating a "new file from selection" from a selected alignment consensus sequence
• Added Open Recent Project and Create Project actions in the Projects kebab menu
• Add Fluorescent Protein CDS mEos3.1 to Common Features Database
• Streamlined the Design Synthetic Construct dialog where primers are not present by removing the primers tab, primers button from side toolbar, and Hybridization Options link in the 
• Allow selecting and copying the text in html formatted windows, synch as summary of Tm calculation methods or alignment algorithms
• Updated various 3rd party tools:
  • io_lib updated to 1.14.15
  • Parasail updated to 2.6.1
  • Qt updated to 6.2.12
• Dragging a tab onto a lowered window will raise it after a delay so that the tab can be dropped onto it.
• Reduced the left margin in Sequence view and moved the translation direction indicator closer to the sequence.
• Streamlined the options provided when right clicking aligned sequence content
• Streamlined context menu for features and primers in ancestral sequences

Bug Fixes

• Fixed stability issues when opening or  working with files with extensive history on Windows
• Corrected feature segment order in some reverse strand features in circular sequences imported from GenBank and Geneious
• Fixed a crash that could occur on Windows when aligning 100 kb+ sequences to a reference sequence
• Fixed bug where consensus sequences over ~25,400 bases were truncated when exporting
• Export file format options are now provided when exporting the consensus for a multiple sequence alignment that has no gaps.
• Disallow exporting the consensus for multiple sequence alignments that contains gaps using the SnapGene format
• Fixed a hang which that could occur when using “New File from Selection” with some alignments
• Improved stability when opening large files
• Accurately report Parasail version
• Improved New File pane on low resolution displays
• Improved updating the mouse pointer when resizing the split view
• Ensure the Align to Reference button in the side toolbar is shown when the view is split
• Fixed bugs with dragging out selections in the Edit DNA Ends dialog
• Improved stability when quitting while using a Flexera license
• Fixed an issue where moving a lone file in a folder in the file and folder panel by clicking and dragging it also moved the folder it was in.
• Fixed issue when exporting sequences where the specified file extension was not preserved if it was allowed but not the default extension for the file format.
• Ensure the project window is raised to the top after merging all windows.
• Improved placement of windows and other controls when using multiple screens.
• Ensure tabs dragged out of a window are placed on the screen on which they are dropped.
• Fixed issue where selecting a folder that contains a single file resulted in the file being opened in a tab.
• Fixed bug that prevented including ('s and )'s in an unquoted query when searching a Project
• Fixed an issue with including tab and other space characters other than the regular space character in a quoted query when searching a Project search
• Fixed a regression where the New File pane did not auto populate the name with contextual information when copying and pasting a region or feature from an open sequence.
• Ensure the "Transfer Features" checkbox in the New File pane is automatically checked when copying and pasting from an open sequence.
• Fixed an issue where Canceling out of Save All showed nonsensical filenames for sequences that have never been saved when Show Details was clicked.
• Updated link to QNtp in the About dialog
• Fixed various issues with encoding the molecule type on the LOCUS line  when exporting to GenBank
• Insert spaces left of the sequence name on the LOCUS line  if it is less than 16 characters when exporting to GenBank
• Fixed a rendering issue with some drop down menus on Windows
• Fixed an issue where a transformation strain specified in the Change Methylation dialog was not reflected in the Description panel
• Fixed an issue where context menu action in History View to unhighlight a restriction site resulted in removing highlighting all  restriction sites 
• Improved stability when making/editing protein features in protein alignments
• Remove Highlight and Clear Highlighting context menu actions for aligned sequences as these commands did not work and make no sense for an aligned sequence since the position of the cut site will be different from the reference sequence.
• Fixed various issues where using the context menu to hide or remove enzymes in aligned sequences did not work, or doing so in the reference sequence did not result in the aligned sequence updating, and vice versa.
• Removed context menu actions to copy the feature translation for aligned sequences since it did not work and doing so would be problematic as the entire feature, and thus its translation, may not be visible due to trimming.
• Improved stability when circularizing single stranded sequences
• Improved tabs bar when horizontal space is limited by dropping tabs and showing a More button.
• Improved which selections result in suggesting the Assemble Contigs action