Version 1.3

By August 23, 2012Release Notes From Blog

New Functionality

  • SnapGene can now open Clone Manager .cm5 files.
  • SnapGene can now open FASTA archives. The FASTA importer has also been improved to decode sequences descriptions and accession numbers.
  • SnapGene now simplifies the display of complex primer-template duplex loops. Accurate melting temperatures are still based on the most energetically favorable duplex structures. If you would like to view the full structures you can restore this behavior under Preferences → Primers.
  • SnapGene now automatically flips fragments when performing InFusion™ Cloning and Overlap Extension PCR. In addition, SnapGene will now automatically choose the appropriate primers to amplify the fused product when performing Overlap Extension PCR.
  • You can now export either rich or simplified GenBank files, the latter of which lack color, directionality, cleavage arrows and segment information.
  • You can now import primers from Vector NTI .oa4 oligo archives and FASTA sequences and archives.


  • You can now align to multiple sequence files at once using the renamed View → “Align with Sequence Traces” command.
  • Improved automatic hyperlink creation when importing from other file formats.
  • Improved opening GenBank files exported from Clone Manager.
  • Dramatically speed up refreshing Map and Enzymes Views when thousands of features or N-stretches are visible.
  • Sped up opening multiple files.
  • Improved display of discrepancies and poorly called bases while viewing alignments.
  • Improved display of primer length, melting temperature, and number of binding sites while using the PCR, Overlap Extension PCR, and InFusion Cloning dialogs.
  • Enhanced the new version available dialog to display screenshots and descriptive text that summarizes the major functionality in a newer version.
  • Improved the behavior when finding enzymes, features and primers within Sequence and Map views.
  • In addition to A, G, and R, you can now also add a single C, T, and Y while using the Edit DNA Ends dialog.
  • Updated the common features database to over 317 unique standard common features.
  • Added NEB’s “1 Kb Extend DNA Ladder”
  • Added “Agilent Technologies” and “MoBiTec” to the sequence author menu in the Description Panel.
  • When exporting a map for the 2nd time, the default format is now the last format used.
  • You can now upgrade from a free trial to the paid version before your free trial expires by using a new “Enter New Registration Code” button in the registration dialog.
  • On OSX the launch dialog now returns when all windows are closed. If you would like to restore the previous behavior (where once closed the launch dialog does not return) you can uncheck this option under Preferences → General
  • Enhanced the Windows installer to check for running copies of SnapGene during installation. If present you now get a chance to quit them before proceeding with installation instead of getting error messages about being unable to install various files.
  • Now displaying more descriptive error message if unable to contact the server or some other error takes place while activating, importing from GenBank, fetching a reference from PubMed, etc.
  • Removed alarming yellow template is already linear message when performing InFusion™ Cloning with a template that is already linear.
  • Various alignment enhancements.

Bug Fixes

  • Fixed various glitches that could occur when attempting to create/save files with filenames that contain invalid characters.
  • Fixed various bugs with the “Browse…” action in the Simulate Agarose Gel and PCR dialog’s template menu.
  • Fixed various bugs with auto-completing enzyme names while using the Simulate Agarose Gel, cloning, and other manipulation dialogs.
  • You can now use File → Print from the Simulate Agarose Gel dialog.
  • Fixed a bug where the jump to the previous/next mismatch buttons in the Align dialog would not always work.
  • Fixed various bugs with the Select Range and Go To commands while using the Align dialog when the alignment wraps around the numerical origin.
  • You can now use Cmd+W to close all modeless dialogs (e.g. the launch dialog) on Mac OS X.
  • Fixed a bug where when importing features from another file it was possible to end up with duplicate copies if a given feature is present more then once in the target sequence.
  • Fixed a bug with saving modifications to the sequence author.
  • Fixed a bug with highlighting the appropriate strand when displaying DNA matches that partially overlap a sticky end.
  • Fixed a bug with activating a copy of SnapGene when an older outdated or expired license is already present on a Windows system.
  • Various other software license improvements and bug fixes.
  • Fixed a bug that could result in the wrong primer being replaced or the application to crash when editing a primer and renaming it to replace another primer.
  • Fixed a reported crash when using the insert symbol dialog.
  • Fixed a bug where not all sequences were always imported when opening Vector NTI .ma4 archives. (Reported by Tomas Bos)
  • Fixed various bugs with painting Enzymes View’s mini-map ruler.
  • Fixed a bug where after browsing to choose a file to import primers from, that file was not added to and listed in the recent primer lists pull down menu when using the import primers form a list dialog again in the future.
  • Fixed a bug with displaying bottom bound primers that have multiple overlapping non-hybridized regions.
  • Fixed a bug where after using Select All to select all primers within Primers view, it was usually impossible to deselect individual primers using Cmd+Click.
  • Fixed a bug where when using the InFusion Cloning → Insert One Fragment dialog it was not listed as an open window. On Windows the Launch dialog could also be shown on top.
  • Fixed a bug where when a linear template is chosen, selecting an enzyme site would automatically check the “Linearize with restriction enzymes” option even though it was disabled.
  • Fixed a bug with transferring features when amplifying fragments that could result in features being replicated.
  • Fixed various bugs with decoding content from rich text (.rtf) encoded files.
    (Reported by Wilfried Rossoll)

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