SnapGene Version 2.8.0

SnapGene 2.8.0 was released on July 01, 2015.

Overview

Version 2.8 adds new capabilities and display options, and refines existing controls.

Minimap for Sequence View

An interactive minimap in Sequence view provides an overview for navigating the DNA sequence.

Show/Hide Feature Labels

In Map view, a new button provides options for the display of feature labels.

Splice to Remove Introns

Introns can be removed in a single step from an mRNA or coding sequence feature.

Re-use an Action Window

A cloning or PCR window can be left open after generating a product, allowing related procedures to be simulated more easily.

Digest a Linear Vector

When a linear vector is supplied to an “Insert Fragment” dialog, the vector can be digested with restriction enzymes.

Prioritize Display of Individual Features

In the Add/Edit Feature dialogs, a feature can be prioritized for display in maps.

More Options for Sequence Trimming

Choose from seven levels of trimming stringency for aligned sequence traces.

Delete Trimmed Bases

After automatic or manual trimming of low-quality sequence trace data, the trimmed bases can be deleted to produce a cleaner alignment display.

Improved Display of Insertions

When an aligned sequence contains an insertion relative to the reference sequence, the insertion is now shown as a triangle in Map view.

Export Grayscale Maps

For publications or reports that do not permit color, SnapGene maps can now be exported to bitmap formats as grayscale.

New Functionality

• Added an interactive minimap overview to Sequence view.
• Enabled Map view to display either external plus internal feature labels, or only internal feature labels, or no feature labels.
• Added a "Splice to Remove Introns" command.
• Enabled cloning and PCR dialogs to remain open after generating the product, so that related procedures can be simulated quickly and easily.
  (Requested by Alejandro Sarrion)
• Modified the Insert Fragment(s) dialogs to enable digestion of a linear vector.
  (Requested by David Bikard and Seth Goldman)
• Enabled individual features to be prioritized for display in maps.
  (Requested by Guiliang Tang, Ignacio Ferrés, Goran, and Thomas Branson)
• Added a "Delete Trimmed Bases" command for cleaning up the display of alignments.
  (Inspired by Michael Lynge Nielsen)
• Modified the display of aligned sequences in Map view to show insertions as inverted triangles.
  (Requested by Michael Lynge Nielsen)
• Enabled maps and history to be exported as grayscale images.
  (Requested by Jennifer Tomczak and Novozymes)
• Added a "Hide Aligned Sequence" context menu command for Map and Sequence views.
• Added Lowest, Lower, Higher, and Highest stringency trimming options for aligned sequence traces.
  (Requested by Wulf Dirk)
• Added an "Open Recent" cascading menu to the top toolbar and the Dock menu on OS X.
• Added an "Import from GenBank" command to the Dock menu on OS X.
• Added a "Copy Map Label" context menu action.
• Added a three finger tap gesture to look up enzyme information without modifying the selection.
• Enabled bzip2 (bz2) compressed content to be opened directly.

Enhancements

• Improved history colors when flipping the sequence, adjusting the numerical origin, renumbering the bases, or changing the methylation.
  (Suggested by Devin Strickland)
• Moved the aligned sequence tooltips in Map view to above the aligned sequences.
  (Suggested by Karl Brune)
• Improved the display of alignment gaps in Map view.
• Sped up starting the application and showing manipulation dialogs.
• Dramatically sped up the decoding of large archive files.
• Sped up topology detection.
• Sped up the opening of gzip (gz) compressed content.
• Improved the opening of large FASTA archives and gz files.
• Added file icons for the "Please choose", "Recent Files", and Windows menus.
• Listed keyboard shortcuts in the Find menu.
• Enhanced primer names and stems to turn red when mousing over an alternative binding site.
• Modified Map view to show the sequence as two strands when custom DNA colors are visible.
• Added "GenScript" to the Sequence Author list.
• Added O'RangeRuler™ ladders from Thermo Scientific.
• Added UBPBio ladders.
• Updated the restriction enzymes and common features databases.
• Various textual, color, and alignment enhancements.

Fixes

• Fixed a rare issue where the application could hang if an aligned sequence had no trace data and began with a non-matching N.
  (Reported by Arthur Fridman)
• Improved the import of very large archives.
  (Reported by Tamunonengiye-Ofori Lawson)
• Enabled copy/paste of a primer-primer selection as a Find query.
  (Reported by Michael Lynge Nielsen)
• Improved the behavior of the "Replace Original with Aligned" command.
  (Reported by Sarah Prewitt)
• Fixed various issues with displaying restriction sites when viewing a primer binding site in a circular sequence near the numerical origin in the Add/Edit/Duplicate Primer dialogs.
  (Reported by Devin Strickland)
• Fixed a stability issue if the current license expires while the software is in use.
• Accelerated the display of feature pliancy and selection in Lines mode of Enzymes view.
• Improved the import of text files with non-UTF file encodings (e.g., MacRoman).
• Configured an Undo of a sequence edit to clear prior "Find" results.
• Modified the behavior of the Back/Forward buttons in the Restriction Enzymes dialog to be simpler and more logical.
• Prevented auto-complete from inappropriately listing headings and actions in the Sequence Author control in the Description Panel.
• Fixed a stability issue when opening a .dna file not created with SnapGene.
• Fixed a stability issue when moving, copying, and deleting files.
• Prevented prior history colors from remaining visible after Undo of a sequence edit.
• Ensured that an unsaved set of chosen enzymes will always be restored when opening a document.
• Fixed a rare stability issue with showing the Genetic Codes dialog.
• Fixed a stability issue with computing translations for features with introns.
• Removed duplicate entries in the "Choose from" menu in the "Choose Enzymes" dialog.
• Fixed a rare issue where a download progress dialog could be shown while the New Version Available window is visible.
• Fixed a stability issue when using a context menu to remove an aligned sequence.
  (Reported by Karl Brune)
• Made the Make/Edit/Duplicate Primer dialogs more compressible so that they fit completely on small screens.
  (Reported by Kasey Day)
• Fixed a rare stability issue.
• Improved “primer” feature import from VNTI .ma4 archives to show the imported items as primers.
• Ensured focus transfer to the next window down when the top window is closed.