SnapGene Version 2.6.0

SnapGene 2.6.0 was released on December 02, 2014.

Overview

Version 2.6 adds new capabilities and improves existing ones.

TA and GC Cloning

TA and GC Cloning

An efficient interface allows you to simulate PCR amplification followed by cloning into TA, UA, and GC cloning vectors. See the tutorial video for details.

U Overhangs

You Can Use U's

SnapGene now allows U to be inserted in place of T near the ends of linear sequences. For example, a U in a PCR primer will generate a U in the amplified product.

Linearize

New Circularize/Linearize Options

With a linear sequence, you can select an internal restriction fragment to be circularized. With a circular sequence, you can place the cursor at any location and then linearize.

Edit Features

Edit Multiple Features Simultaneously

When multiple features are selected, parameters such as feature type and directionality can be specified for all of the features at once.

Alignment Arrows

More Informative Alignment Arrows

In Map view, the arrows showing aligned sequences now indicate the nonaligned ends as well as all mismatches and indels.

Resolution

Flexible Resolution for Exported Maps

DNA maps can be exported at any desired resolution.

EMBL Format

Support for EMBL Format

SnapGene can now read and write DNA sequence files in EMBL format.

New Functionality

  • TA, GC and UA cloning.
  • Support for U's in DNA sequences.
  • You can now edit the color, type, directionality, and translated state for multiple features at a time.
    (Requested by Tian Chi and Wulf Dirk)
  • Non aligned ends are now shown when viewing alignments in Map view.
    (Requested by Devin Strickland, Bryan Strouse, and Janel Lape)
  • All mutations are now visible when viewing alignments in Map view.
    (Suggested by Wulf Dirk)
  • You can now linearize a circular sequence at the location of a placed cursor.
    (Requested by Diane Chauliac)
  • You can now directly circularize a selected restriction fragment. When attempting to circularize a PCR product with single 3' base overhangs, SnapGene now offers to remove those overhangs in order to make circularization possible. Finally, history colors are now generated when circularizing.
    (Requested by Dan Kraut)
  • You can now export Map and History views at various resolutions. Improved support exporting transparent images. When exporting as TIFF, SnapGene now uses LZW compression and transparent TIFF's are now also supported.
  • You can now export Map view, History view, and agarose gels to the EMF vector format on Windows.
  • When copying a map or history to the clipboard a vector form of the data is now stored on the clipboard so elements can be moved or edited when pasting into programs like Microsoft Office or Adobe Illustrator.
  • Open EMBL formatted sequences and export sequences using the EMBL format.
    (Requested by Iñigo Lasa, Colin Adrain, and Kobi Benenson)
  • You can now export sequences to the DDBJ format.
  • Added "λ DNA – HindIII/φX174 DNA – HaeIII Digest" ladder
    (Requested by Brian Ayre)

Enhancements

  • SnapGene can now automatically annotate common features when opening FASTA sequences and archives.
    (Suggested by Willem-Jan Waterreus)
  • The "Anneal Oligos" dialog now auto populates if two primers are selected in an open sequence when the window is shown.
  • You can now include features added by NCBI when importing from GenBank.
  • Added the full template name to the tooltip shown when mousing over the list in the Simulate Agarose Gel dialog if the name is truncated within the list.
  • When exporting History view to PDF, we now use Portrait instead of Landscape orientation since it usually fits better that way.
  • Improved the default size of the "Manage Enzyme Sets" dialog.
  • After linearizing at any position other than the origin, Map view now defaults to showing a broken circle.
  • Various font, color, and textual enhancements.

Bug Fixes

  • Fixed a bug that could prevent printing with network printers on Windows.
    (Reported by Cassandra Diegel)
  • Improved exporting to GenBank to better conform to the standard and resolve various warnings when converting to EMBL when uploading files to EMBL-EBI.
    (Reported by Kobi Benenson)
  • Fixed a bug where trace data for short aligned sequences could be shown at too low a resolution.
    (Reported by Miguel Cardoso de Brito)
  • Fixed a bug that could result in primers not being transferred to an amplified product when using PCR based dialogs.
    (Reported by Mathias Friedrich)
  • Fixed a bug that prevented opening some MacVector files.
    (Reported by Hilary)
  • Fixed a crash that could occur while simulating various manipulations.
    (Reported by Angika Basant)
  • Fixed bugs with visualizing insertions at the numerical origin and replacing the original with the aligned sequence under such circumstances.
    (Reported by Jason Niehaus)
  • Fixed a bug where if no attB inserts are to be amplified by PCR, when clicking "Choose attB Primers" SnapGene should pop up a message instead of doing nothing.
  • Fixed a bug with deselecting primers in Primers view by Cmd/Ctrl clicking.
  • Fixed a bug where primers were lost when using the "Replace Original with Aligned → Make New File" command.
  • Fixed a bug with replacing and existing license file on Windows.
  • Fixed an erroneous error message that would show up (invalid license file) if installing the license file fails.
  • Improved exporting to SVG. (The bounds of the exported content are not set so scrolling, if necessary, is much improved).
  • Fixed a bug that resulted in "Copy Map" to sometimes be disabled while viewing Map view.
  • Fixed a bug where the default filename when using Save As was sometimes incorrectly set to "Untitled" on Mac OS X 10.9 and later.
  • Fixed a bug that prevented opening GenBank files when filtering files in the Open File dialog to "Sequence Files".
  • Fixed a bug where when simulating a manipulation using an open document with unsaved case changes, those changes were not reflected in a resurrected ancestor.
  • Fixed a bug where unsaved case changes were not properly reflected when exporting to FASTA or plain text.
  • Fixed a bug when annealing oligos I's were not converted to N's as expected.
  • Fixed a hang when deleting bases from a single strand from an end that is currently covalently closed while using the Edit DNA Ends dialog.
  • Fixed a bug where when enlarging the Edit DNA Ends dialog, additional space not used entirely for viewing the upstream and downstream ends.
  • Fixed a bug where if a mixture of colored and non-colored features were selected when triggering "Features → Feature Color" no option should be checked by default.
  • Fixed a cosmetic glitches with rendering ovals and header buttons.
  • Fixed a bug where an error message was shown twice when trying to open a GenBank file that does not contain a nucleotide sequence.
  • Fixed a crash that could occur when importing a GenBank archive that contains on or more empty sequences (aka sequences without nucleotide data).
  • Fixed a crash that could occur while viewing raw sequence trace data.
  • Fixed a bug where if enzymes were off and you opened and then canceled out of the Choose Enzymes dialog SnapGene would offer to turn on showing enzymes.
  • Various stability fixes.
  • Fixed various memory leaks.

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