SnapGene Version 5.2.0

SnapGene 5.2.0 was released on October 12, 2020.

Overview

Version 5.2 provides visualization and performance enhancements. Updates include GC content visualization, support for finding similar DNA sequences, simulation of supercoiled DNA migration in agarose gels, support for ssDNA sequences, and Sequencher file import.

GC Content Display

A GC content color or line plot can now be displayed in Map view, and bases can be colored by GC or AT in Sequence view.

Find Similar DNA Sequences

When searching for DNA sequences, imperfect matches containing gaps or mismatched bases can be found, and search performance has been optimized.

Supercoiled DNA Migration

When simulating agarose gels, the migration of uncut circular sequences can be visualized, and supercoiled MW markers can be used.

ssDNA Sequences

A single-stranded DNA (ssDNA) sequence can now be created or imported, with support for feature annotation and sequence manipulations.

Optimized History View

When editing sequences, the history is compressed to allow efficient storage as well as Undo for large sequences.

Additional Protein Feature Types

The set of supported protein feature types has been extended, including support for the misc_feature type.

Sequencher File Import

Sequencher files can now be imported into a SnapGene collection.

New Functionality

• Enabled visualization of GC content as a color plot in Map view or base colors in Sequence view.
  (Requested by Michael Brooks, Max Garwood, Robb Stankey and others)
• Added support for finding similar DNA sequences with mismatches or indels compared to the search query.
  (Requested by multiple users)
• Added support for simulating the migration of supercoiled DNA molecules in agarose gels using TBE, TAE or SB buffer.
  (Requested by multiple users)
• Added support for single-stranded DNA (ssDNA) sequences.
  (Requested by John O'Brien and others)
• Enabled import of Sequencher project files (*.spf).
  (Requested by May Cindhuchao, Heather McFarlane, and Usua Oyarbide)
• Enabled "Undo" for edits in large sequences.
• Added DNA ladders from DyneBio.
  (Requested by Dae-Geun Song)
• Added supercoiled MW markers from ELPIS BIOTECH and New England Biolabs.
• Added BsmBI-v2 to the list of enzymes available from New England BioLabs.
• Added fields for username and email address in the license registration dialog.

Enhancements

• Optimized storage of history for the following operations: Change Methylation, Change Transformation Strain, Set Origin, Flip, Insert/Delete/Replace, Linearize, Circularize.
  (Requested by Dan Lysko, and by others who complained about large files)
• Updated the supported protein feature types by adding new types (NonStdRes, Protein, Precursor, SecStr, Het, CDS, gene, misc_feature, unsure, variation), promoting Region subtypes to types, and adding new Site and Bond subtypes.
  (Requested by Sanofi)
• Added a note in Features view to indicate the presence of internal stop codons in a translated feature.
  (Inspired by Tom Hamer)
• Enhanced the Preferences tools to allow more flexible default options for displaying ORFs.
  (Requesed by Caroline Reiss)
• Enabled carrying over feature qualifiers when creating a protein sequence using "Make Protein" or "Reverse Translate".
  (Requested by Katherine Geromini)
• Added the option to merge segments when using "Make Protein" on a multi-segment DNA feature.
• Added a "Hide noncutters" check box in the Choose Enzymes dialog.
  (Inspired by Bruce Lahn)
• Enabled importing features from any supported file type when using "Import Features from a SnapGene File".
  (Requested by Greg Perry)
• Enabled more flexible batch conversion of chromatogram traces to other formats.
  (Requested by Arthur Fridman)
• Improved search performance for large DNA sequences.
• Configured the minimap to show both scrolled areas when two copies of Sequence view are visible.
• Updated the format of the Preferences dialog, and added an "Agarose Gels" tab.
• Added the option to designate a new collection as the Main Collection.
• Enabled saving imported online sequences directly to a collection.
• Added shortcuts in a collection Overview for navigating to the DNA Files, Protein Files, or Miscellaneous Files sections.
• Enabled symbols to be entered in search queries when searching SnapGene Online Sequences.
• Increased the size of the length indicator in the map label at the "Small" font size.
• Consolidated all Fisher MW Markers for agarose gels in the Fisher Scientific set.
• Configured the Nonredundant Commercial enzyme set to include similar enzymes that differ by methylation sensitivity.
• Configured SnapGene to show the Launch dialog on macOS when the SnapGene icon in the Dock is clicked, if no SnapGene windows are open.
• Changed the icon for enabling interrupted circle format for a linear DNA sequence in Map view.
• Configured the "Export Map" and "Export History" options to be always enabled.
• Improved the wording of various menu options and dialogs to provide greater clarity and consistency.
• Added a message informing the user that files can be dragged into the list when using Align Multiple Sequences.

Fixes

• Fixed an issue that prevented cloning dialogs from allowing the use of hidden enzymes.
  (Reported by Mily Ron)
• Corrected an issue in "Protein Search" whereby terminal stop codons were not included in the search query.
  (Reported by Mike Xie)
• Ensured that edits in an alignment window do not cause inappropriate scrolling.
  (Reported by Beth Lawrence)
• Corrected an issue that could prevent alignment of a high-quality sequence trace.
  (Reported by Jessie Saul)
• Ensured that the "Find" control in the Enzymes view chooser always shows a message to indicate if the enzyme is not in the chosen set.
• Corrected an issue in which U's in overhangs resulting from linearizing were not preserved.
• Configured "Select All" in the trace viewer context menu to actually select all.
• Ensured that History view reflects changes after editing DNA ends.
• Ensured that case changes in the "Find" entry field are preserved when the search is executed.
• Ensured that imported RNA alignments are converted to DNA rather than protein alignments.
• Corrected the license inactivity countdown to displays seconds rather than milliseconds.
• Ensured that the "Accession Number:" label remains next to its entry field in the collection Search dialog.
• Ensured that a "Sequence Name" search in the Protein Files area of a collection also searches the map labels and aliases.
• Corrected an issue that resulted in alignment and collection windows not showing unsaved changes in the title bar on Windows and Linux.
• Ensured more consistent sorting of enzymes in the Choose Enzymes dialog.
• Streamlined the substitution matrix options presented when computing pairwise alignments.
• Ensured that open alignments can be used as profiles when computing new alignments.
• Corrected an issue that could result in the "Kind" column disappearing when viewing a collection.
• Ensured that crisp screenshots are shown when detecting updates.
• Improved import of the full publication date from PubMed.
• Made various stability fixes.