SnapGene Version 2.4.0

SnapGene 2.4.0 was released on May 28, 2014.

Overview

Version 2.4 improves the display of feature names in maps, adds more versatile support for blunting sticky ends, enhances the history display, adds controls for managing feature and primer lists, and provides new options for exchanging data with other file formats.

External Feature Names in Maps

For a feature in the first row of a map, if there is not enough room to show the name next to the feature, the name is now displayed outside the map.

Versatile Blunting of 5' Overhangs

A 5' overhang can be blunted by either filling in (e.g., with Klenow) or chewing back (e.g., with mung bean nuclease).

More Information in History View

History view now displays how a sticky end was blunted, and lists the names of primers used during PCR.

Check/Uncheck All Features or Primers

When features or primers are either viewed in a DNA file or imported from a list, a new menu button allows global checking or unchecking of the listed items.

Export to Vector NTI® Format

A DNA sequence can be exported to a GenBank-style file that is optimized for import into Vector NTI®.

Read Primer Data from Clone Manager

Clone Manager individual primer files (.pd4) can be opened directly, and primer collection files (.px5) can be used for import into SnapGene.

New Functionality

• A 5’ overhang can be blunted by either filling in or chewing back.
  (Requested by Berislav Lisnic and Andreas Toft Sorensen)
• A DNA sequence can be exported to a GenBank-style file that is optimized for import into Vector NTI®.
  (Requested by Wulf Dirk Leuschner, Scott Dooley and Alper)
• Clone Manager individual primer files (.pd4) can be opened directly, and primer collection files (.px5) can be used for import into SnapGene. (Requested by Oliver Sinfield and Jo Marie Bacusmo)
• You can now manually trim an aligned sequence by selecting the range to be trimmed off, then clicking "Aligned Sequences → Trim Selected Range".
  (Inspired by Alex Zelenskyy)
• You can now linearly ligate up to four fragments.
  (Requested by Emmanouil)
• You can now search for the amino acid "X" by using quotes.
  (Requested by Keoni Gandall)
• The MW of amino acid selections are now show in the selection bar.
  (Requested by Deepak Patil)
• For a feature in the first row of a map, if there is not enough room to show the name within or along side the feature, the name is now displayed outside the map.
• History View now displays how a sticky end was blunted.
• History View now lists the names of primers used during PCR.
• When features or primers are viewed in a DNA file, imported from a list, or when detecting common features, a new button at the top left provides options for quickly checking and unchecking the listed items.
• If you hold Alt/Opt, you can now "Copy Transparent Map" or "Copy Transparent History". This works for the Edit menu, the top toolbar button menu, and right click context menus in Map and History views.

Enhancements

• Improved detection of Gateway recombination sequences.
• Improved opening of GenBank files exported by Vector NTI including sequence name, author, creation and modification dates, and feature names.
• Improved opening of GenBank files exported by Serial Cloner including feature visibility, names, colors, directionality, and descriptions.
• Improved support for QHD displays on Windows.
• When exporting the default directory is now the last directory content was exported to. In addition the last format used is now the default format.
  (Suggested by Wulf Dirk)
• The yellow messages that indicate a number of enzymes, features, or primers are not displayed on map view due to limited space now show a tooltip when moused over that indicates which enzymes, features, or primers could not be shown.
• Added support for the "Candidate Division SR1 and Gracilibacteria" genetic code.
• Sped up alignments of fairly large sequences (e.g. 40 Kbp) against very large reference sequences (e.g. chromosomes).
• Added links to Translations and Alignments tutorial videos.
• Various color and textual enhancements.

Bug Fixes

• Fixed glitches with opening GenBank files that contain tab characters.
  (Reported by Wulf Dirk)
• Improved decoding feature names from GenBank files.
  (Suggested buy Wulf Dirk)
• Fixed a bug where features might not be transferred to the product when simulating PCR using overlapping primers that mutagenize the sequence.
  (Reported by Dan Kraut)
• Fixed a bug where PCR based dialogs would sometimes complain that a primer pair was not suitable for PCR when despite overlapping binding sites PCR was possible because the template was circular.
  (Reported by Dan Kraut)
• Removed nonfunctioning File and Edit menus from Make/Edit/Duplicate Primer dialogs on Windows.
  (Reported by Scott Dooley)
• Fixed a bug where if a non-native file was chosen as the template or vector in any of the manipulation dialogs, features would not be transferred to the product while simulating cloning, PCR, etc.
  (Reported by Rocky Cranenburgh)
• Fixed a bug where long sequence and ancestral sequence names could be cut off when shown in History View.
  (Reported by Alok Shenoy)
• Fixed detecting custom 7 and 8 bp custom common features.
  (Reported by Donelson)
• Fixed issues with annotations are not shown, would you like to display them type messages on Windows.
  (Reported by Wulf Dirk)
• Fixed a bug where horizontal scrolling switched tabs in the Preferences, Map & Sequence Options, Primer and Chromatogram Data dialogs.
• Disabled the "Select All" button while using the "Add Features/Primers" and "Detect Common Features" dialogs since selections are not allowed.
• Fixed a bug that made it impossible to use a non-native file as the vector in the InFusion Cloning and Gibson Assembly dialogs.
• Fixed a bug that could result in a crash when editing feature translation options for 1 and 2 bp features.
• No longer listing translation qualifiers (codon_start, transl_table, translation) in Features View for features that are not marked for translating in Sequence View.
• Fixed various bugs with opening some rich text encoded files.
• "Apply this genetic code to existing features" did not properly update feature translations, mark the sequence as modified, or support Undo/Redo.
• Fixed a glitch where an empty COMMENT or DEFINITION was sometimes exported to GenBank formats.
• The "Reset Warnings" button in the Preferences dialog is now disabled if no warnings have been turned off.
• Fixed a bug that resulted in features now being shown for the current sequence in History View after transforming into another strain, changing the methylation, or other changes that don't result in actually changing the underlying DNA.
• Disabled "Edit → Select Range" while using the Detect Common Features and Import Features/Primers dialogs.
• Fixed various glitches with shift-clicking fragments while using the Simulate Agarose Gel dialog.
• Fixed the MW for amino acids "X" and "B"
• Fixed a bug where history colors might now shown when using mutagentic primers to simulate PCR.