SnapGene Version 2.7.0

SnapGene 2.7.0 was released on March 05, 2015.

Overview

Version 2.7 adds new capabilities, and enhances the software to take advantage of the latest operating systems and high-resolution displays.

DNA Base Colors

Choose colors for DNA bases, with the option of coloring the two strands differently.

Primer Colors

Primers can now be color coded, with the color indicators visible across different views.

Frame Check for Fusions

If a cloning procedure will generate an out-of-frame fusion between translated features, SnapGene provides a warning.

Compatibility and Resolution Updates

SnapGene has been updated to ensure full compatibility with OS X 10.10 Yosemite and Windows 10, and to display crisp images on high-resolution monitors. Due to these enhancements, version 2.7 requires OS X 10.7 or later.

Linear Gibson Assembly®

Use Gibson Assembly® to generate not only circular vectors, but also linear products.

Paste Formatted Sequences

When creating a new DNA file, paste a FASTA- or GenBank- or EMBL-formatted sequence, and SnapGene will import the sequence and annotations.

More Options for Agarose Gels

The gel simulation now supports agarose concentrations up to 4%, a gel image can be copied directly to the clipboard, and molecular weight markers from PHENIX Research and others have been added.

Make Features from Aligned Sequences

Aligned sequences can be converted directly to features.

Read Files from DNADynamo

Annotated DNA sequence files created with DNADynamo can now be opened directly with SnapGene.

New Functionality

• Substantially improved the look and feel on high-resolution displays.
• Enabled DNA base colors to be specified.
• Enabled primers to have different colors.
• Enabled multiple primers to be edited simultaneously to specify color, case, etc.
• Added a new Add Copied Primers command (Cmd+Opt+R).
  (Requested by Karl Brune)
• Expanded the Gibson Assembly® options to allow for creation of linear products.
  (Requested by Vincent Gaggioli)
• Added warnings for out-of-frame translated features when simulating cloning or ligation procedures.
• Enabled pasting of content encoded in GenBank, EMBL, or FASTA format into the New DNA File and Insert|Replace Bases dialogs. Annotations will be preserved as if you had opened the file directly. Similarly, you can align with a copied FASTA, GenBank or EMBL sequence. The default name for a pasted New DNA File or aligned copied sequence has also been improved.
  (Requested by Allan Drummond, Karl Brune, Cornelius Miething, and Christel Aebischer)
• Added an importer that allows DNADynamo files to be opened directly in SnapGene.
  (Requested by Maria Deak)
• Enabled opening of files with gzip compressed content (e.g., .fa.gz).
• Enabled copying of an agarose gel image or fragment list to the clipboard.
  (Requested by Wulf Dirk)
• Expanded the range of agarose concentrations supported when simulating gels.
  (Requested by Robert Getty)
• Added several MW ladders.
  (NZYTech ladders requested by Daniel Osório)
  (PHENIX Research ladders requested by Robert Getty)
• Enabled the creation of features from selected aligned sequences via a new "Make Feature[s] from Selected Sequence[s]" command in the "Aligned Sequences" menu.
  (Suggested by Andy Crouse)
• Added “Enter|Exit Full Screen" commands to the Window menu on OS X.
• Added a "Show Chromatogram Data" context menu command for aligned sequence traces.
• Added “Copy Feature Name" and "Copy Primer Name" context menu commands.
  (Requested by Wulf Dirk)
• Added a window list to the Dock menu on OS X.
  (Requested by Di)
• Added commands to the jump list shown when right-clicking the application in the taskbar on Windows 7 and later.

Enhancements

• Improved detection of lacZα.
  (Requested by Joëlle Fourment)
• Enhanced the display so that when mousing over an enzyme that cuts more than once, the stems connecting other sites for the same enzyme also turn red.
  (Suggested by Angika Basant)
• Reduced the size of text and features in History view maps to facilitate showing more annotations in those maps.
  (Inspired by Damien Douchi)
• Added an option on Windows to automatically minimize the Launch dialog when all windows have been closed.
  (Suggested by Ron Godiska)
• Added the "NEB Stable" transformation strain.
  (Requested by András Tálas)
• Added the option of selecting gaps within features by Opt/Alt-clicking them.
• Implemented a check to prevent TOPO® TA cloning with phosphorylated primers.
• Updated the TOPO® TA and Gateway® Donor vectors.
• Enhanced the ruler for translated features in Sequence view to show a break if there is a discontinuity in the translation numbering.
• Removed the "Enzymes" tab from the TA and GC Cloning dialogs because restriction enzymes are never used.
• Added a "PCR and Mutagenesis Tutorial Video" command to the "Actions" menu.
• Improved the visibility of warnings shown within the status box at the lower right of manipulation dialogs.
• Improved the display of ladder fragment lengths in simulated agarose gels.
• Added Cmd+Shift+[ and Cmd+Shift+] to switch lanes in the Simulate Agarose Gel dialog. The swipe gesture can now be used as well.
• Configured fragments in agarose gels to animate to their new positions when changing the agarose percentage.
• Improved the look and feel on OS X Yosemite. Unfortunately, we can no longer support OS X Leopard and Snow Leopard.
• Converted SnapGene to a 64-bit application on Mac OS X.
• Implemented extensive icon, textual, color, and rendering enhancements.
• Added support for queueing when using a shared license.

Fixes

• Fixed an issue where importing primers from a list beginning with a "Name Sequence" line would generate an error message before displaying the Add Primers dialog.
  (Reported by Pascal Drevet)
• Enabled Shift-clicking of letter codes to generate a selection from two different translated in-frame features.
  (Reported by Rocky Cranenburgh)
• Enabled the import of primers containing U's or I's from a list.
  (Reported by Stephanie Ruiz)
• Fixed issues with opening and pasting DNA sequences containing colons and other punctuation.
  (Reported by Ron Godiska)
• Fixed issues with displaying origin-spanning and other complex multiple sequence alignments.
  (Reported by Pavel Chubukov, Chris Katanski, and Jenna Christensen)
• Fixed a crash when opening files with a one or more blank lines at the top.
  (Reported by Monfort Pineda Asun)
• Fixed an issue where the Save As dialog sometimes did not default to the correct filename on OS X 10.9 and 10.10.
  (Reported by Nick Bogard)
• Improved the import of primers from a Vector NTI® database and of GenBank files exported from Vector NTI®.
  (Reported by Cor Breukel)
• Fixed an issue where a printed agarose gel did not always list the length of amplified fragments.
  (Reported by Alice Fok)
• Improved the simulation of Gibson Assembly® when one or more fragments have 5' overhangs.
  (Reported by Shouqiang Cheng)
• Improved the simulation of In-Fusion® cloning when one or more fragments have 3' overhangs.
• Added a check to recompute the melting temperature when toggling the "5' Phosphorylated" check box in the Make/Edit/Duplicate Primer dialogs.
• Added a check to ensure that SnapGene does not run into trouble by trying to open bz2 compressed content.
• Prevented a hang that could occur when trying to find data within an empty file.
• Improved the accuracy of showing history colors after deleting an arbitrary range of bases.
• Fixed an issue where various Edit menu actions (e.g. "Copy Top Strand") sometimes were not enabled when a selection was present.
• Fixed a crash that could occur upon renaming, moving, or deleting an open file while using a modal dialog (e.g., Edit Primers).
• Improved pliancy for Inserts in the TA Cloning and Restriction Cloning overviews.
• Maintained consistency by showing a non-specified Gateway® vector in black instead of gray in the cloning overview.
• Ensured that after changing the transformation strain, the "Hide/Erase" button in History view would become enabled.
• Fixed an issue where tooltips shown in the New/Insert/Replace Dialog and a few other places would continue to be shown if the window containing the associated label was hidden or closed while the tooltip was visible.
  (Reported by Melissa Stokes)
• Improved file association registration on Mac OS X.
• Fixed an issue with displaying the correct sequence when a reverse aligned sequence is shown as a double-stranded sequence.
• Prevented a crash that could occur upon closing a document while using the Edit and Duplicate Primer dialogs.
• Prevented a crash that could occur when closing an open document with unsaved changes that is currently in use in a manipulation dialog.
• Turned off changing a combobox selection using the mouse wheel.
• Fixed a regression that prevented restriction sites close to the numerical origin from being shown in History view.
• Fixed an issue with showing partial filling in when using the "Choose dNTPs" dialog.
• Enabled the use of Cmd+Shift+[5-9] to switch tabs in cloning dialogs with many tabs.
• Improved drag selection from a site in the main view in Enzymes view to a site in the minimap or vice versa.
• Ensured that agarose gel fragment endpoints are printed correctly when the template numbering is set to count from something other than 1.
• Prevented a crash that could occur when pressing the left arrow key when a button has focus.
• Prevented a crash that could occasionally result from the core search algorithm.
• Fixed an issue in Map and History views where using the "Edit Map Label" and other context menu commands sometimes resulted in the map being copied to the clipboard as well.