SnapGene Version 2.2.0

SnapGene 2.2.0 was released on November 25, 2013.

Overview

Version 2.2 focuses on addressing some of the excellent suggestions from our customers.

Extra Sorting Options for Enzymes

In Enzymes view, the enzyme list can be sorted either by location of the first site, or by distance from the selection to the nearest site.

New Controls for Gibson Assembly®

During automated primer design for Gibson Assembly, you can choose either a fixed number of overlapping bases or a target Tm for the overlap.

Enhanced Agarose Gel Simulations

Gel lanes now show either restriction digests or PCR amplifications. Up to 20 lanes can be displayed. Use the “Apply to All Lanes” button to choose enzymes once for the whole gel.

More Improvements to Multiple Alignment

An updated alignment algorithm gives better results for repeated sequences. The trace display is continuous for single-base gaps.

Print Alignments

Alignments can now be printed in several formats.

Suppressor Genetic Codes

To support synthetic biology and other applications, you can set a particular stop codon to encode a “wild-card” amino acid.

Hide “Start” and “End” Labels

For linear sequences, the “Start” and “End” labels in the map can be hidden.

Open Files from Visual Cloning

SnapGene and SnapGene Viewer can now read files created by Visual Cloning.

New Functionality

• Display a MW marker in any lane when simulating agarose gels.
  (Suggested by Virgile Adam and Brandon)
• Display fragments produced by PCR when simulating agarose gels.
  (Suggested by Raymond Molloy)
• Click "Apply to All Lanes" to digest all lanes with the same enzymes when simulating agarose gels.
  (Suggested by Dana Nadler)
• Support for 10-20 lanes when simulating agarose gels.
  (Suggested by Zhonghua)
• Reset all lanes when simulating agarose gels.
  (Suggested by David Scalzo)
• Adjust the electrophoresis time using the mouse wheel when simulating agarose gels.
• You can now print alignments from Sequence View as well as the Align With a Sequence Trace dialog.
  (Requested by Kobi Benenson and Tomo Inobe)
• SnapGene now supports multi-sequence GenBank archives files.
  (Requested by Laure Quintric, Markus Sack, Roy Granit and Natalia Skawinska)
• Added a "Import ApE Feature Library" command to the "Import/Export" menu in the Browse Common Features dialog. (Requested by Alper)
• You can now select fragments by Cmd/Ctrl clicking between sites in Enzymes View
  (Suggested by Matt Neale)
• You can now sort enzymes in Enzymes View by location or distance to the cursor or selection using the pull down button right of the "Sites" header.
  (Suggested by Matt Neale)
• When zooming, swiping left/right will initially scroll the display, then switch over to panning the zoomed range.
  (Requested by Alex Zelenskyy)
• Added Amber, Ochre, and Opal genetic codes.
  (Requested by Ohad Vonshak)
• Specified enzymes that do not cut the template are now listed in the Simulate Agarose Gel fragments list.
  (Suggested by Tom Serwold)
• You can now specify the exact overlap length and split the overlap the between the vector and fragments when designing primers for Gibson Assembly. The overlap can now be designed up to 100 bp.
  (Suggested by Tom Folliard)
• SnapGene can now open files produced by Visual Cloning.
  (Requested by Nuria Andreu)
• You can now show/hide Start/End labels us a new command in the View menu.
• Added a right click context menu for aligned sequence names at the lower left of Sequence View for hiding, renaming, exporting and removing sequences.

Enhancements

• Improved responsiveness on Mac OS X 10.9.
• Significantly improved and faster alignments.
• Only showing breaks in trace data for gaps > 1 bp in length.
  (Requested by Sandra Taylor)
• When editing custom common features, you can now change the feature type and toggle translating in Sequence View.
  (Suggested by Wulf Dirk)
• Improved opening exceptionally large archive files.
  (Requested by Evan Williams)
• Improved the alignment algorithm, especially when working with related sequences.
• Adjusted format when exporting to GenBank to improve compatibility with less sophisticated parsers.
• Added "Set Default MW Marker..." and "Edit MW Markers List..." buttons when viewing agarose gel lanes that are set to use a MW Marker.
• Added fragment count to MW marker lane tooltips in the Simulate Agarose Gel dialog.
• Improved printing of sequence trace quality data.
• When opening non-native files, feature types are now corrected to match the case in the GenBank standard as necessary.
• If a non-standard genetic code is used to translated a feature, the "Nonstandard genetic code" message shown in the Add/Edit Feature dialogs is now a clickable link that pulls up the translation options.
• Improved responsiveness of agarose gel widget.
• Various textual, color, and layout enhancements.

Bug Fixes

• Fixed recognition sequence for PI-SceI
  (Reported by Xiaoxi Liu)
• Fixed bugs with performing searches while viewing flipped sequence traces.
  (Reported by Ota Hlavacek)
• Fixed a bug where it was not possible to traverse into folder aliases while using the Open/Export/Save As dialogs on Mac OS X.
  (Reported by Pascal Drevet)
• Fixed a crash that could occur when right clicking within empty space in some views. (Reported by Erin Adams)
• Fixed a bug where Map View become unresponsive if the sequence contains a very large number of primers that only bind one or twice.
  (Reported by Gongwei)
• Fixed a bug where when clearing an agarose gel lane, the lane should remain selected.
• Fixed potential crashes while using the Simulate Gel dialog.
• Fixed a bug that sometimes prevented displaying "Shift-click to select a second primer" in PCR based manipulation dialogs.
• Fixed a bug where "< Please Choose >" could be listed twice in a source pull down menu.
• Fixed a regression where the I-beam cursor was shown in linear map view when well above the strand.
• Fixed a bug where while using the "Simulate Agarose Gel" dialog a "Specify different enzymes" or other red messages might appear below enzyme controls when they don't actually apply.
• Fixed a potential crash when computing sequence trace quality data.
• Fixed a bug where tooltips in the Simulate Agarose Gel dialog did not properly indicate fragment endpoints when working with linear templates that don't count bases from 1.
• Fixed a bug that prevented additional toolbar messages from being shown until the next time the program was started.
• When customizing standard common features the "Options" button is now hidden.
• Horizontal mouse wheeling while over a tabs bar no longer changes tabs.
• Fixed a bug that could result in varying dates or times being shown in the footer across various pages in a document.
• Fixed a bug where printed content slightly shifted left on each successive page.
• Fixed bugs that could result in crashes when attempting to open very large non native files.
• Fixed a bug where after duplicating a lane all summaries in the list would collapse.
• Fixed a bug where trace data sometimes wasn't shown for the first few aligned bases in an aligned sequence.
• Fixed a bug that could result in an infinite loop when displaying toolbar messages.
• Disabled "Tools → DNA Molecular Weight" while viewing a sequence trace.
• Fixed bugs with disappearing gap-spanning features when only the gap is visible.
• Fixed bugs with gap-spanning feature names disappearing when the gap is partially visible.
• Fixed a bug where the numerical origin was not maintained properly when using Gibson Assembly / In-Fusion Cloning and using primers that overlap to amplify/extend the Vector to effectively use a site of insertion.
• Fixed a bug where asterisks were not shown for non-standard stop codons in the Genetic Code Tables dialog.
• Fixed a crash that could occur while hovering over or double or right clicking over the Enzyme or Sites columns in Enzymes View.
• Sped up and fixed bugs with laying out sequence trace curves.
• Fixed a bug where while viewing an alignment in Sequence View, if you highlighted a base just before a gap the green box would extend through the gap.
• Fixed a bug where short aligned sequences were not visible in Map View when viewing a large reference sequence.
• Fixed a bug where if a bottom-bound primer that hybridizes to the very end of a linear sequence was shown in a broken circular map, the stem and label was incorrectly drawn at the beginning instead of the end of the sequence.
• Fixed bugs with highlighting bases and painting selections adjacent to or spanning gaps or the cursor if placed at a gap while viewing alignments in Sequence View.
• Fixed bugs with displaying primers and history colors across gaps while viewing an alignment in Sequence View.
• Fixed a bug where the "Hybridiziation Parameters" command should be disabled when using a manipulation dialog and the visible template is not loaded.
• Fixed various bugs that would result in crashes when opening very large files.
• Fixed a crash that could occur when undoing arbitrary edits.
• Fixed a crash that could occur while changing the methylation state while viewing an alignment.
• Fixed a bug where enzyme block state was not refreshed for aligned sequences when changing the methylation state.
• Fixed a crash that could occur when switching between simplified and full duplex structure modes while a manipulation dialog with unspecified templates was open.
• Fixed a regression that prevented the "To perform alignments, please upgrade to SnapGene" message from displaying properly in in Sequence Viewer.
• Fixed a bug with optimizing reverse alignment gaps.
• Fixed a bug that could prevent aligned sequences from properly vertically resizing when expanded, collapsed, or switching between trace and double stranded views.
• Fixed a bug where aligned sequences viewed as double stranded sequences did not show enzymes/translations according to the view options properly by default.
• Fixed a bug that resulted in a slow down when identifying ORF's in large sequences containing N-stretches.
• Fixed a bug with showing references in the Description Panel.
• Fixed a bug that resulted in various menu actions not being properly enabled while specifying DNA in various controls such as the New, Insert, and Replace Bases dialogs.