SnapGene Version 2.1.0

SnapGene 2.1.0 was released on September 16, 2013.

Overview

Version 2.1 includes a number of improvements and new capabilities.

Visualize Gaps in Alignments

If an aligned sequence has a gap, you can now see the position of the gap in Map view.

Jump Past Gaps in Alignments

New buttons enable you to jump past gaps from one aligned region to the next.

Show DNA Molecular Weight

The molecular weight of a DNA construct can be displayed in an accessory window. If you select a region of the DNA, the molecular weight of the selection is displayed as well.

Primer Molecular Weights

The molecular weight of each primer is now displayed in Primers view.

Export a Selection

Export a selected region, such as an individual feature, to GenBank or other formats.

New Functionality

• Gaps in alignments are now visible in Map View.
• Added "Next/Previous Aligned Region" buttons for navigating an alignment in Sequence View.
• Alignment controls can now be horizontally resized.
  (Suggested by Adrienne Luoma)
• You can now customized the MW Markers menu
  (Suggested by Dan S.)
• Added a "Show DNA Molecular Weight" Command.
  (Requested by Jeffrey Carey)
• You can now export sequence selections directly to a file.
  (Requested by Alex Zelenskyy and Izhak Kehat)

Enhancements

• While scrolling past a large gap in an aligned sequence in Sequence View the sequence no longer disappears.
• Enhanced automatic scrolling in response to clicking the "Next/Previous Discrepancy" buttons in Sequence View.
• The navigation buttons while viewing an alignment in Sequence View can now be used to jump to non-aligned regions of the reference sequence.
• Added a "Show/Hide Enzymes" command to the Enzymes menu for quickly toggling the display of enzymes in Sequence and Map Views.
• Added various shortcuts for alignments to the "Keyboard Shortcuts" dialog.
• Added a "Save Enzyme Set" button to Enzymes View.
• Various optimizations that make aligning with multiples sequences faster as well as opening files that contain multiple embedded aligned sequences.
• The Home and End keys can now be used to scroll vertical scroll areas.
• Added "Oxford Genetics" to the list of predefined sequence authors.
• Enhanced suggested file names when using "New File from Selection"
• Matches within translations are no longer returned when performing a search while using Features View.
  (Suggested by Keoni Gandall)
• Lowered the minimum PCR primer Tm to 45°C
  (Suggested by Keoni Gandall)
• Added suggested tips and information to the toolbar in SnapGene Viewer.
• Enhanced summary string when using Blast DNA for enzyme, and primer based selections.
• Added the legend and fixed the pinch icon in the Gestures dialog on Windows.
• Removed "Insect Cells" and "Plant Cells" from the "Natural DNA" menu in the description panel since natural DNA comes from specific species.
• Sequence View now auto scrolls to selected aligned sequence after selecting a sequence using Map View.
• Removed red pliancy and instead clicking anywhere on a features/primer in the import and detect common features dialogs now toggles importing the clicked item.
• Enhanced detection of common features to allow for 1 bp omissions at either end of certain feature types.
• When deleting/replacing the visible end of an aligned sequence, we now delete/replace the actual end of the aligned sequence if the end was not visible due to trimming.
• Added controls for setting the default transformation strain to the "Edit Strains List" dialog.
• The text edit within the New/Insert/Replace dialogs should now be far more responsive when working with and reverse complementing large sequences.
• Various textual, icon, and alignment enhancements.

Bug Fixes

• Fixed hang on XP when OKing out of Edit Feature dialog on Windows XP while viewing a linear map.
  (Reported by Ayelet)
• Fixed a regression in 2.0 that resulted in blunt restriction sites not being displayed at the end of Sequence View lines.
  (Reported by Lucas Almendra)
• Fixed a bug where the Primers dialogs incorrectly reported the number of annealed bases when simplified primer-template duplexes are shown.
  (Reported by Devin Strickland)
• Fixed a bug with properly displaying origin-spanning primers in the Primer dialogs.
  (Reported by Devin Strickland)
• Fixed a bug that prevented pasting large copied selections (> 1 Mbp) into the New, Insert and Replace Bases dialogs.
  (Reported by Siddarth Arumugam)
• Fixed a crash that could occur while detecting common features.
  (Reported by Jordan Ang)
• Fixed brief flashes that could occur while horizontally scrolling sequence view while viewing alignments.
• Fixed a bug that could result in a hang when loading XML encoded data.
• Fixed bugs with pliancy in Features and Primers Views.
• Fixed a bug where alignments mode was not turned off automatically when manually switching from a linear to a circular map representation.
• Fixed a bug that prevented SnapGene from automatically detecting a software update is available.
• Fixed a bug where when expanding an aligned sequence, viewing it as a double stranded sequence, the sequence would stop scrolling to the left once the last trimmed aligned base was visible.
• Fixed the following bugs when viewing reverse aligned sequences as double stranded sequences: -Enzyme tooltips and sequence endpoint labels showed the incorrect cut position -Sequence endpoint labels were sometimes incorrectly shown when aligned sequence was trimmed or sequence end was not aligned. -Start/End labels should be swapped -Incorrect number shown at the right end
• Fixed a small memory leak when changing the default MW markers.
• Fixed bugs with setting the default MW markers
• Fixed a glitch where items in the "Edit Strains List" dialog were selectable.
• Fixed a hang that could occur while viewing zoomed maps with aligned sequences.
• Fixed a crash that could occur while using the Mutagenesis dialog.
• Fixed a bug that could result in trimmed trace data being displayed right of aligned called bases.
• Fixed a bug where when undoing an edits to aligned sequences the trimmed range was not properly restored.
• Fixed a bug where when editing an aligned sequence the length was not updated at the lower left when expanded within Sequence View.
• Fixed bugs with automatically scrolling to aligned sequences.
• Fixed a bug where a crash could occur while viewing an alignment.
• Fixed a bug that could result in annotations being lost if the application crashed in the middle of saving out changes to a document.
• Fixed a bug with restoring the trimmed range after undoing a deletion or replacement on an aligned sequence.
• Fixed a bug that prevented inserting bases at the very end of a sequence trace or aligned sequence, or the very beginning of a reverse aligned sequence, or undoing a deletion or replacement that effectively requires an insertion at such a location.
• Fixed a bug where after performing an insertion, deletion, or replacement on an aligned sequence, the view could scroll improperly.
• Fixed a bug where if an aligned sequence that contains a selection was unchecked the view would scroll. Similarly, when undoing such an action the original selection is now restored.
• Fixed a regression in 2.0 with properly displaying long fixed line widths that require horizontal scrolling in Sequence View.
• Fixed a glitch where sometimes while interacting with Sequence View and viewing an alignment, content would stop expanding properly to use vertical space.
• Fixed a bug where when viewing a wrap-around alignment the aligned sequence would never disappear while scrolling when not technically visible.
• Fixed a bug that prevented properly scrolling to an aligned sequence that wraps around the numerical origin when selecting it in the list or using the "Next/Previous Aligned Sequence" buttons.
• Fixed a potential crash while scrolling MSA mode and viewing an aligned sequence as a double stranded sequence.
• Fixed a bug with displaying alignments that wrap around the numerical origin where no aligned region wraps around the origin.
• Fixed a bug with displaying alignments after resetting the numerical origin, flipping the sequence, or undoing such actions.
• Fixed a bug where while using a manipulation dialog if you closed a Noncutters dialog, then minimized and restored the manipulation dialog the Noncutters dialog would reappear.
• Fixed various glitches where tapping enter while using the Add/Remove controls in Enzymes view did not respond as expected.
• Page Up/Down now can be used to scroll Sequence View while viewing a multiple sequence alignment.
• Added missing window resizing size grip from lower right corner of the Import Features/Primers and Detect Common Features dialogs.
• Fixed a bug where if you made a DNA selection in Map View, then selected an aligned sequence, when switching to Sequence View the view auto scrolled to the DNA selection instead of the more recently selected aligned sequence.
• Fixed a bug that could result in trace curve data being displayed beyond the end of an alignment.
• Fixed various bugs with undoing deleting aligned sequence bases.
• The Sequence View ruler no longer displays tick marks and number right of the last zoomed base.
• Fixed glitches that could result in duplicated ancestors being stored within a file or in rare cases lost ancestors.
• Fixed a potential bug where when saving out changes to file annotations non volatile data (e.g. DNA) could potentially be lost in the process.
• Fixed a bug where when using the "Insert Fragment(s)" dialog if the insertion was the exact same size as the fragment to be replaced, features in the replaced ranged were not removed as they should be.
• Fixed a bug where when inserting a flipped fragment that was already linearized the features in the insert were not flipped as they should be.
  (Reported by Pieter J deJong)