SnapGene Version 5.1.0

SnapGene 5.1.0 was released on April 12, 2020.


Version 5.1 provides enhanced flexibility for displaying and annotating sequences. Updates include an improved layout for linear maps, an optional split view for sequence windows, more versatile controls for enzyme visibility, and links between related folders in different areas of a SnapGene collection.

Better Linear Maps

Enzyme sites and other annotations in a linear map are now allowed to overlap, thereby reducing map height while preserving legibility.


Optional Split View

A DNA or protein sequence window can be split to show two different views, or two versions of the same view.


Enzyme Visibility Controls

Like features and primers, individual enzymes can now be shown or hidden using check boxes.


Links Between Collection Areas

When a SnapGene collection stores related files in the DNA Files, Protein Files, and Miscellaneous Files areas.


Flexible Choice of Reference Type

When adding references to the Description Panel, a variety of reference types are now available.


Adjustable Threshold for Feature Detection

When importing features from another SnapGene file or detecting common features, the match threshold can be adjusted between 80-100%.


Batch Edits in Collections

A SnapGene collection now supports batch edits of multiple files for flipping sequences, importing features or primers, detecting features or primers, performing BLAST searches, and specifying entries in the Description Panel.


Optional Stripes for “A” Traces

In a sequence trace file, the “A” trace can be displayed with stripes to support researchers with color vision disabilities.


Pre-defined “Type IIS Enzymes” Set

Type IIS enzymes, which are used for Golden Gate assembly, can be displayed using a pre-defined enzyme set.


New Functionality

  • Enabled DNA and protein sequence windows to be split to show two views, one above the other.
    (Requested over the years by multiple users)
  • Added support in the Description Panel for various reference types including books, database entries, patents (which can be imported from online databases), theses, web links, and more.
  • Configured /citation qualifier values to link to specific references, which are accessible via tooltips and clickable links in Features view.
  • Added optional page number entries for /citation qualifiers.
  • Enabled enzyme visibility to be adjusted in Enzymes view using check boxes, mirroring the controls used for Features and Primers views.
  • Enabled flexible feature detection with an adjustable similarity threshold when importing features from another file.
  • Added support for exporting aligned sequence trace data using a tab-separated format.
    (Requested by Yves Girerd-Chambaz)
  • Enabled BLAST for multiple selected sequence files in a collection.
    (Requested by Charles Dozois)
  • Added a pre-defined enzyme set for Type IIS enzymes.
  • Enabled import of features or primers from another file, or detection of common features, for multiple selected DNA files in a collection.
    (Requested by Michael Gotrik)
  • Enabled simultaneous flipping of multiple selected DNA sequences in a collection.
  • Added support for linking folders of the same name in different areas of a collection, with "Go to ..." shortcuts for switching between related folders in different areas.
    (Requested by Mily Ron)
  • Enabled the "Make Protein" and "Reverse Translate" commands, when operating within a collection, to save the output files to a linked folder in a different area of the collection.
  • Added support for batch replacement of Description Panel fields for files in a collection.
    (Requested by Samuel Tremblay-Belzile)
  • Added MW markers from Nacalai Tesque.
    (Requested by Tomonori Hoshino)
  • Added MW markers from FroggaBio.
    (Requested by Michael Ostrovski)
  • Added MW markers from Newmarket Scientific.
    (Requested by Sabrina)
  • Added the remaining TrackIt™ MW markers from Thermo Fisher.
    (Requested by Slava Gurevich)
  • Improved feature tooltips when using compact mode in Sequence view.
    (Requested by Bandar)


  • Reduced the height of linear maps by enabling items to be superimposed without sacrificing legibility.
    (Requested by Vishal Chaudhari)
  • Changed the defaults to show HF® and FastDigest® information in the Restriction Enzymes dialog, while allowing these defaults to be adjusted.
    (Requested by Silvana Jirka)
  • Enhanced the File > Export cascading menu to enable export of multiple files or a list of files from a collection.
    (Requested by Gurumoorthy Krishnamoorthy)
  • Added support for a color attribute when importing features from GFF3 format.
    (Requested by Matthew Kirk)
  • Added support for specifying the line break characters when exporting to text file formats.
    (Requested by Tim Fallon and Tom Chappell)
  • Enabled long map labels to span two lines in circular Map view.
    (Requested by Chun Cao)
  • Configured Sequence view to retain visibility of the scrolled region when toggling horizontal scrolling.
    (Requested by Kengo Adachi)
  • Enhanced the flexibility of code number display in collection lists.
    (Requested by Tim Nierhaus)
  • Added a keyboard shortcut for "Import UniProt Sequences".
    (Requested by James Wright)
  • Enabled colors in multiple sequence alignments to be copied to the clipboard.
    (Requested by Monir Ejemel)
  • Added support for importing Vector NTI Express Designer databases
    (Requested by Dave Karig)
  • Provided the option to differentiate "A" traces using a striped pattern for users with color vision disabilities.
  • Provided an adjustable similarity threshold for detecting common features.
  • Enabled the "Make Protein", "Reverse Translate", and "New File From Selection" commands to save the output files to the same collection.
  • Allowed the genetic code to be specified when converting a selection in a DNA alignment to a protein alignment.
  • Ensured that when sorting by Code Number or Alias in a collection, any files with blank entries are placed at the end of the list.
  • Converted SnapGene to a 64-bit application on Windows, thereby improving performance and stability.
  • Ensured that scrollbars are shown only when necessary in Map, Sequence, and History views.
  • Improved the wording in the Restriction Enzymes dialog to make it clearer when a supplier offers multiple variants of an enzyme.
  • Changed the License Agreement dialog so that it is no longer modal, and added support for printing or saving this document using keyboard shortcuts.
  • Made various textual, color, and icon enhancements.


  • Configured the Find control to show bottom strand results when using compact format in Sequence view.
    (Requested by Bandar)
  • Prevented extra line breaks from appearing after export of some qualifier values to GenBank and EMBL formats.
    (Reported by Karen Ross)
  • Ensured that all controls in alignment dialogs can be translated into Japanese or Chinese.
  • Ensured that collection folder names for selected items never appear in List view.
  • Enabled scrolling up using Shift + Spacebar in Sequence view.
  • Fixed paging up and down using Function + Up/Down keys, and scrolling to the start or end of the sequence using Function + Left/Right keys.
  • Ensured that ancestral blunt cutters can be shown in green in History view after import from Vector NTI® or other file formats.
  • Prevented unnecessarily asking to add methylation when specifying "Escherichia coli" as the Source for a Natural DNA sequence.
  • Corrected an error with internal array data when editing trace sequences.
  • Ensured that linearizing or circularizing a DNA sequence populates the Sequence Author field with the default author.
  • Configured Enzymes view to show enzyme sites in red upon mouseover in both the main view and the lower map.
  • Corrected codon frequencies for reverse directional ORFs.
  • Ensured that the Description Panel flows to the bottom of the window when zoom controls are shown.
  • Fixed various issues with importing primers into DNA files in a collection.
  • Ensured that the map label in a circular map never overlaps features.
  • Disable menu File > Export > History when no history exists in sequence file.
  • Fix Blasting selected primer in a collection file.
  • Fix Tools > Blast Selected Protein with a collection file.
  • Ensured that the Previous button in the Find controls is shown in blue only if the Shift key and no other key is pressed.
  • Adjusted the behavior for sequence traces so that mousing over an ambiguous base darkens the curves for multiple bases.
  • Prevented accented characters from being accidentally inserted into a DNA or protein sequence when holding down letter keys on macOS.
  • Improved the foreground color within features while using compact Sequence view.
  • Improved feature pliancy while using compact Sequence view.
  • Fixed an issue in which pressing the Shift key resulted in a button changing color in the "Import Features from a SnapGene File" and "Detect Common Features" dialogs.
  • Improved the look and feel of controls for Enzymes view on Windows.
  • Preserved formatting when creating hyperlinks.
  • Improved horizontal alignment of values shown in the Properties tab for protein sequences.
  • Enabled proper export of /citation qualifier values to GenBank, GenPept, and EMBL formats.
  • Ensured that suppliers remain selected after dragging them in the Enzymes tab of the Preferences dialog.
  • Updated the MW calculation for a full sequence in the DNA Calculations window after 5' phosphates are added or removed.
  • Enabled bottom strand matches to search queries in Sequence view when using compact mode.
  • Ensured that qualifier selections in Features view are cleared when selecting features or transferring focus to the Description Panel.
  • Configured a collection to show and select imported files even when those files are not in the currently chosen category.
  • Fixed an issue that could result in labels for Site features not being shown entirely within a protein sequence window.
  • Improved the horizontal placement of names and connecting lines for site features in Sequence view.
  • Fixed an issue in which selections in Features and Primers views sometimes remained blue after focus was transferred to the Description Panel.
  • Disabled controls for setting the DNA color when using either compact Sequence view or Map view with features on the DNA line.
  • Fixed issues with displaying enzymes that make two double-stranded cuts when a site is near the end of a linear sequence.
  • Improved stability when importing Vector NTI Express Designer enzyme names
    (Reported by Dave Karig)

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