SnapGene Version 2.3.0

SnapGene 2.3.0 was released on March 20, 2014.

Overview

Version 2.3 enhances the multiple alignment capabilities of SnapGene in important ways. The major changes are listed below.

Mutations in Aligned Sequences

An aligned sequence can now be expanded to show how features, primers, and ORFs differ compared to the original sequence. For translations, the modified amino acids are marked in red.

Draggable Ends of Aligned Sequences

Drag handles allow the ends of an aligned sequence to be adjusted.

Replace Original with Aligned

Select one or more aligned sequences that match one another, and replace the corresponding regions in the original sequence.

Direction Indicators for Horizontal Scrolling

When Sequence view is scrolled horizontally, arrows display the orientation of directional features.

Enzyme Set Export

Export the noncutters or any other enzyme set to a text file.

New Functionality

• Aligned sequences can now be trimmed manually.
• Features, primers, ORFs are now shown when viewing aligned sequences as double stranded sequences.
• Letter codes that overlap discrepancies are now shown in red while viewing aligned sequences as double stranded sequences.
• You can now replace bases in the reference sequence using one or more aligned sequences.
  (Requested by Jared Bailey and Veronique Zennou)
• You can now use boolean logic (or, not) when searching for DNA sequences. Added a "Search Tips" dialog that explains how degenerate bases and boolean logic can be used when searching for DNA and protein sequences, as well as how to perform various searches for enzymes, etc.
• You can now export an enzyme set as a list.
  (Suggested by Lynne Harris)
• You can now export Noncutters.
  (Suggested by Devin Strickland)
• You can now copy the reverse complement of a primer sequence.
  (Suggested by Allan Drummond)
• Added a variety of alternate commands that are available by holding Alt (Windows) or Opt (Mac). These include: Close All Without Saving
  (Suggested by Seth Goldman) Detect Common Features in the Selection
  (Suggested by Wulf Dirk) Minimize All Zoom All
• Added DNA MW Markers for Bioneer, Canvax Biotech, and Geneaid.
• You can now shift/control click aligned sequence arrows at the lower left of Sequence View to select multiple aligned sequences.
• You can now deselect restriction sites and primer binding sites by Cmd/Ctrl + clicking.

Enhancements

• You can now click and hold to move aligned sequences up and down, or adjust the enzyme supplier order.
  (Suggested by Seth Goldman)
• You can now set the "Detect Common Features" and "Import Features/Primers from Another File" dialogs to not show details by default.
  (Suggested by Wulf Dirk Leuschner)
• Increased the maximum primer length from 150 to 200 bp.
  (Requested by Seth Goldman)
• Reduced the minimum common feature length from 8 to 6
  (Requested by Malon Kit)
• Added directionality indicators to features in Sequence View while using infinite scrolling if a features directional endpoint is not visible and space permits.
• Speed up loading documents with aligned sequences and showing alignments in general.
• Improved and speed up the alignment algorithm
• Improved the detect common features algorithm
• Improved circular plasmid detection
• Improved searching for enzymes
• Improved how single-base gaps are shown when viewing aligned traces.
• Various optimizations that result in faster loading, zooming, and refreshing linear maps.
• Added a "Remove" button at the lower left of the "Browse Common Features" dialog while viewing custom features.
• Added "Canvax Biotech" and "Cellecta" to the "Sequence Author" menu in the description panel.
• Improved the default set of DNA MW Markers
• Added a new "ORFs Only" icon
• Improved default focus when using the Simulate Agarose Gel dialog.
• Improved right click context menu's for feature/primer name, search, and other text controls.
• Added "SnapGene Bucks..." link to SnapGene (Mac) and Help (Windows) menus.
• You can now click on ladder and transformation strain names (or methylation information) to check/uncheck them in the Edit Strains/Ladders dialogs.
• Scale factors now animate back to 1.0x if clicked while viewing a sequence trace.
• Clicking "Preferences" in "Summary of Calculation Methods" now transfers focus to the checked radio button for changing duplex complexity.
• Streamlined context menu for "Summary of Calculation Methods" and "License Agreement" dialogs.
• Converted the format used for exporting and importing enzyme sets to plain text.
• Added links to Gibson Assembly and In-Fusion Cloning tutorial videos to their cascading menus.
• Various color, textual and stability enhancements.

Bug Fixes

• Fixed a bug that could prevent many menu actions from being enabled while using the Simulate Agarose Gel dialog.
  (Reported by David Scalzo)
• Fixed a crash that could occur when attempting to import primers from a list or open a sequence archive.
  (Reported by Oliver Sinfield)
• Fixed a glitch that prevented opening some Jellyfish files.
  (Reported by Joao Goncalves)
• Fixed a bug that allowed primer controls to scroll vertically using the mouse wheel or clicking and dragging up and down. Also improved their vertical height.
  (Reported by Allan Drummond)
• Corrected the recognition sequence for FaiI.
  (Reported by Pieter de Jong)
• Fixed a bug with copying an ORF translation if it begins at the end of the sequence but the first letter code is actually one or more bases in from the end.
  (Reported by Mark Fisher)
• Disabled "New File from Selection" for aligned sequence selections.
• Fixed a minor bug with showing proper history colors.
• Fixed a minor glitch with displaying the base under the mouse in the single line view of the reference sequence in Sequence View while viewing an alignment.
• Fixed a minor bug with sorting enzymes by distance from the selection.
• Fixed a bug with identifying the selection or placed cursor while viewing an alignment.
• Fixed a glitch that could result in some trace data not being displayed while viewing an alignment.
• Fixed a minor glitch with refreshing the features menu while using a manipulation dialog.
• Fixed a bug that could result in primer phosphate groups not being shown while viewing alignments
• Fixed a minor bug that could result in a feature not correctly being reset from using an alternative Start codon when bases were inserted or deleted within the original start codon.
• Fixed a bug with exporting aligned sequences other than sequence traces where N's could show up as -'s in the exported DNA file.
• Fixed various bugs when viewing an aligned sequence as a double stranded sequence when multiple sequences are aligned.
• Fixed a bug with showing the numerical origin when viewing primers that wrap around the numerical origin while using the Add/Edit/Duplicate Primer dialogs.
• Fixed a regression that prevented the "Your copy Expires soon" and "Getting Started" dialogs from showing any text.
• Fixed a potential crash when computing quality measures when dealing with bad trace data.
• Fixed a bug with showing some multiple sequence alignments.
• Fixed a bug where when converting part or all of a primer name to upper or lowercase while using the Add/Edit/Duplicate Primer dialogs, the shown binding site was not updated.
• Fixed a bug with displaying the cursor when placed at the right edge of an aligned sequence.
• Fixed glitches that occurred if you tried to move the cursor or move or extend the selection in an aligned sequence such that it extends or is outside the aligned range.
• Fixed a glitch where when moving the cursor to the very right of the aligned range while viewing an aligned sequence as a double stranded sequence, the view would scroll to the very beginning.
• Fixed a bug where while using Sequence View with infinite scrolling and zooming in it was possible to scroll too far to the right.
• Fixed a bug where newly created files (E.g. New File or manipulation products), if you modified them after they were opened, then undid the change, the window lost it's "modified" state and didn't ask if you wish to save before closing as it should, even though all undoable changes had been undone.
• Fixed a bug that resulted in a selection being shown for an aligned sequence when shown as double stranded when the selection is just upstream of the trimmed range.
• Fixed a bug that prevented showing the green/orange arrows indicating the reading frame for generic translations of aligned sequences.
• Fixed a bug where when scrolling far to the right and viewing translations for an aligned sequence some letter codes were painted on top of each other.
• Under "Sequence Author", changed "5 Prime" to "5 PRIME".
• While viewing an alignment in Sequence View, if you click below the horizontal splitter outside of any aligned sequence, you can once again use the arrow keys to scroll the view, or other key presses to effect the reference sequence.
• Fixed bugs with painting generic translations when zooming.
• If a subscription license is expiring soon, before showing the expiring soon message, SnapGene first attempts to update the license in case the subscription has been renewed already.
• Fixed various bugs with displaying trace data when viewing alignments.
• Fixed a bug where if an operation is selected automatically in History View it was not shown as selected, only history colors were shown.
• Fixed a bug that prevented propagating methylation changes to aligned sequences.
• Fixed the following bugs with reverse aligned sequences: -showing %GC for selections -copying translations
• Fixed bugs with dragging selections over gaps while viewing multiple sequence alignments in Sequence View.
• Fixed a bug where the numerical origin could be shown incorrectly for aligned sequences
• Fixed bugs with displaying selections that wrap-around the numerical origin in Sequence View.
• Fixed a bug with highlighted the matched DNA when searching if the last matched base was the first base in the sequence.
• Fixed a bug where if multiple DNA modifications are performed while using the Edit DNA Ends dialog, the resulting file would get bigger than it should due to embedding the intermediate ancestors.
• Fixed a regression with the mouse position indicator when interacting with the currently sequence map in history view.
• Fixed a bug where if a linear sequence is shown as a broken circle, if you start zooming we need to automatically switch to showing a linear map.
• When copying all or a subset of an aligned sequence, we now properly store the name of the aligned sequence on the clipboard.
• Fixed various bugs with viewing alignments.
• Fixed a bug where an enzyme name in brackets was not cleared when adding a 3' base to a blunt end or removing a 3' overhang.
• Fixed a bug that prevented deselecting features in history view by Cmd/Ctrl + clicking.
• Fixed numbers shown when mousing over bases right of "Original Sequence" in Sequence View while viewing an alignment.
• Fixed a bug where after converting bases to upper or lower case, the change could sometimes revert after saving.
• Fixed a bug with updating the selection in the alignment interface after editing the reference sequence.
• After editing the reference sequence, expanded aligned sequences now remain expanded.
• Fixed a bug that prevented copying or blasting feature run-on translation selections.
• Fixed bugs with placing the cursor or making selections after edits were performed while using the "Edit DNA Ends" dialog.
• Fixed a glitch that allowed content to be selected in the Keyboard Shortcuts and Gestures dialogs when right clicking.
• "Align with Other Sequences..." now logs the last directory content was selected from and using that directory by default when aligning with additional sequences, or opening files in general.
• Arrow heads are now shown correctly in Map View for sequences that align around the numerical origin.
• SnapGene can now be activated and make network connections when sitting behind a proxy server that requires authentication.