SnapGene Version 9.0.0

Overview

SnapGene 9.0 introduces a number of new features, including Primer Databases, making it possible to save primers in a single central location, and reuse these across your sequence files. CRISPR Guide Design enables visualization and scoring of CRISPR guide RNAs directly within SnapGene. Search improvements make it easier to find and display results clearly. A number of improvements have also been made across data views, with side-by-side split view and rotating maps giving more flexibility to sequence views.

Primer Databases

Save your primer sequences from your DNA files, or import primers from spreadsheets, to a central primer database within SnapGene. Labels provide an easy way to organize primers into groups, and manage your primer database. These primers can then be used to annotate your other sequence files, giving an easy way to manage your primer sequences across all your files in a single location.

CRISPR Guide Design

Find and visualize CRISPR guide RNAs directly in SnapGene using a variety of PAM sequences, with results displayed in a convenient table. Score designed CRISPR guides for efficiency and specificity using a number of peer-reviewed algorithms on our secure cloud server. Specificity scoring provides a selection of common genomes to score against.

Search Improvements

Search improvements make it easier to perform searches and identify results across your project folders and primer database. Results are organized by the type of search hit, and clearly show where your result was found.

More Control Over Your Data

Enhancements across data views enable more customization of sequence views. Split view functionality has been extended to support both side-by-side and top-and-bottom views, while map view now supports rotating sequences. Multifile selections now offer the ability to view multiple sequences in map view, giving a clear summary of your files. Improvements to multisequence file import make it easier to manage and convert sequence files into SnapGene.

Detailed Changes

• Introduced primer databases for primer management in SnapGene
  • Introduced primer databases for primer management in SnapGene
  • Added labels for organization of primers
  • Added ability to annotate sequences using primers within the primer database
  • Implemented import into primer database from .csv files, or SnapGene .dna files
  • Enabled export of primer databases in native database or .csv format
• Added CRISPR guide design support
  • Implemented the ability to Find CRISPR guides on sequences under 5 kb in length
  • Introduced the ability to score CRISPR guide RNAs using a selection of peer-reviewed scoring algorithms
• Implemented side-by-side split view
• Improved project search and results display
• Improved import of multisequence files
  • Introduced a new universal import dialog for multisequence files
  • Implemented consistent import behaviours for multisequence files
  • Fixed multi-sequence files getting stuck in Other Open Files without a tab.
  • Fixed issues with WGS accession import
• Improved window resizing for smaller displays
• Improved UniProt import
  • Fully integrated import from UniProtKB
  • Download from UniParc for sequences that have been removed from UniProtKB
  • Fixed multiple issues where misleading error messages were shown when UniProt import fails.
• Introduced multifile map view
• Modernized preferences dialog
• Modernized primers and features tables
• Modernized and enhanced focus (zoom) view
• Added ability to rotate circular sequences in map view
• Added tool to convert GenBank primer_bind features to SnapGene Primers
• Added a preference to make adjusting feature color based on background color optional
• Feature labels can now include length and feature type
• Upgraded ViennaRNA to 2.7.2
• Implemented Machine Access Token support
• Added VectorBuilder Strains to the strains database
• Implemented tab preview popover upon hover
• Added support for /subtype qualifiers on CDS features for Luma users

Additional Changes in 9.0.0b2

• Improved primer database management
  • Updated the Primers menu with additional primer database actions
  • Added a menu item to edit label colors
  • Valid primers are now preselected when the primer import dialog opens
  • Refined the primer database interface
• Refined CRISPR guide design support
  • Guide scoring is now off by default for new searches
  • Refined the CRISPR guide results table
• Improved import of multisequence files
  • Raised the FASTA/FASTQ import limit to 1,000 sequences
  • Added an "Import existing features" option for formats that can carry features
  • SAM, BAM and CEP assemblies containing a single contig now open directly instead of as an archive table
  • Contig assemblies no longer replace the open project folder
• Increased the size limit for sequences shown in multifile map view to 50 kb
• Updated Linux packaging scripts to use https links
• Updated OpenSSL to 3.0.22 and xz_utils to 5.8.3

Additional Changes in 9.0.0b3

• Improved Primer Database management
  • Use default file hybridisation parameters when annotating a file from the primer database
  • Updated messages shown when duplicate primers are detected
  • Duplicate primer action implemented in primer database
  • Support added for editing of primers in the primer database 
  • Primer database menu items now consistent across different menus
• Refined CRISPR design
  • Added project search support for CRISPR sites
  • Added support to export CRISPR sites to TSV
  • Find CRISPR Sites action moved to Tools menu
  • Added validation for searches that are shorter than the target sequence
  • Added the ability to import CRISPR guides from CRISPOR
• Improved multisequence import
  • Sequences with changes now shown in bold
• Added a delay to the project side panel upon hover

Bug Fixes

• Fixed gels loading slowly when recent documents included large sequences.
• Fixed an inability to annotate features in pairwise alignments in SnapGene Viewer.
• Fixed an issue with RNA sequences exporting as DNA (thymine instead of uracil) when exported to plain text.
• Fixed inconsistent font sizes for vector/fragment radio buttons in Golden Gate Cloning.
• Fixed a cut-off percentage value in the amino acid composition table when a single residue is selected.
• Fixed inconsistent and incorrect sequence naming when importing FASTA files.
• Fixed slow, unresponsive-looking GenBank imports by adding a progress bar and the ability to cancel.
• Fixed incorrect Opt/Alt-hover behavior when viewing FASTQ files.
• Fixed file names containing periods being truncated when exporting a gel's fragment list.
• Fixed a crash on Windows when closing the Edit DNA Ends dialog after its document had been closed.
• Fixed a misplaced label in the Mutagenesis dialog.
• Fixed "Align to Reference" incorrectly showing an extra nucleotide in the reference on repeat-heavy sequences.
• Fixed incorrect translations when making an RNA or DNA file from a selection containing CDS features.
• Fixed Sanger-to-FASTQ export incorrectly wrapping sequence and quality lines.
• Fixed the "Show Features" tooltip appearing in the wrong place in some dialogs.
• Fixed occasional PCR failure with valid, overlapping primers on a circular template.
• Fixed an overly bright, distracting panel splitter in dark mode.
• Fixed feature name labels overlapping protein features in map view when bonds are shown.
• Fixed the project window title not correctly reflecting unsaved changes.
• Fixed dragging a folder of SnapGene files into a project doing nothing on Windows.
• Fixed protein charge values above 10% being truncated in the pH dropdown.
• Fixed buggy typing and an incorrect checkbox in the New Sequence dialog after pasting a feature.
• Fixed occasional Gateway Cloning failure when existing primers were present.
• Fixed the "Replace Codons" dropdown incorrectly staying hidden in Choose Alternative Codons.
• Fixed the base number tooltip incorrectly appearing when hovering over the project panel divider.
• Fixed stray characters and hard-to-read text in the Search Tips dialog in dark mode.
• Fixed incorrect symbol colors in the Symbols and Abbreviations dialog in dark mode.
• Fixed map view showing more primer binding sites than intended.
• Fixed feature annotations not mirroring correctly when a vector is flipped during Insert Cloning.
• Updated the hover border color on viewer tabs to match the design system.
• Updated the inactive tab border color to match the design system.
• Fixed RefSeq WGS genomes importing from NCBI without annotations.
• Fixed features being offset by 1 bp after circularizing with NEBuilder HiFi DNA Assembly.
• Fixed cut-off drop shadows on toggle containers.
• Fixed the temperature field in Secondary Structure Settings not auto-selecting its contents.
• Fixed a blank Map tab after saving a protein file created with Make Protein.
• Fixed a crash when undoing changes in the Anneal Oligos dialog.
• Fixed a crash (and hang) when saving a copy of a file with a name differing only in letter case.
• Fixed tooltips flickering on the wrong screen on multi-monitor setups.
• Fixed the wrong file sometimes being selected after double-clicking in the project sidebar.
• Fixed flickering when selecting amino acids within a feature's translation.
• Improved contrast for the unsaved-changes alert icon in dark mode.
• Fixed a bug where downloaded files sometimes failed to automatically appear in project folders.
• Fixed reverse-complement ORFs not appearing in Map view.
• Fixed a crash when creating a new DNA or RNA file with no project open.
• Fixed an odd-looking junction between tab outline lines in dark mode.
• Fixed cut-off table headers on Windows with display scaling enabled.
• Fixed hanging and crashing when editing a primer name in cloning dialogs.
• Fixed long file names not truncating with an ellipsis in the toolbar.
• Fixed tooltip flickering when extending a selection by a single base in compact view.
• Fixed a crash when copying selected bases in a DNA alignment.
• Fixed the info panel incorrectly labeling natural sequences as "Laboratory Host" instead of "Source."
• Fixed a tab showing as modified after undoing all changes.
• Fixed incorrect translations shown with Show Translations when an ORF wraps around the origin.
• Improved the error message that’s displayed when Golden Gate primer design fails due to insufficient overhangs.
• Fixed a crash when renaming an open gel file in Finder.
• Fixed pasting via the right-click menu sometimes pasting text twice on Windows.
• Fixed incorrect strandedness when importing Geneious documents.
• Fixed "Translate the first codon as Methionine" not resetting when the first codon is edited for translated segments spanning the origin.
• Fixed Undo not working from the Edit menu in the Anneal Oligos and Mutagenesis dialogs.
• Fixed the project sidebar not refreshing for folders with Japanese characters in the name.
• Fixed a potential infinite loop when removing duplicate citation references.
• Fixed an unwanted border on the New DNA File text field.
• Fixed several issues rendering watermarks on exported images for SnapGene Viewer users, including stretched, missing, and disabled watermarks.
• Fixed pasting RNA into a New DNA File dialog sometimes failing to switch to RNA mode.
• Fixed hang on startup when a recent document was in a disconnected cloud-synced folder.
• Fixed a crash when clicking a menu item whose control had already been closed.
• Fixed a crash on exit on Windows.
• Fixed a crash while closing a sequence viewer.
• Fixed a crash when loading cached tabs on startup.
• Updated SnapGene Server to support Ubuntu 24.
• Fixed inability to download WGS sequences using NCBI's newer 6-letter accession format.
• Fixed some WGS sequences failing to download due to a sequence count limit.
• Fixed a spurious console warning when making single-stranded DNA from RNA.
• Fixed file changes in project subfolders sometimes not being detected on Linux.
• Fixed a typo in the "CRISPR Plasmids" folder name in the Sample Project.
• Fixed inability to select the sequence row in pairwise alignments when features are shown.
• Fixed vector features being lost after Gibson Assembly when the replacement region spans the origin.
• Fixed trackpad scrolling stopping abruptly in tables.
• Fixed a bug where RNA sequences in FASTA archives were always imported as DNA.
• Fixed a bug where clicking an unsaved gel in the project sidebar sometimes opened a temporary file instead.
• GenBank /anticodon qualifiers are now read and exported correctly.
• Fixed a hang displaying RNA/ssDNA structures in SnapGene Viewer. Users are now prompted to purchase a paid license instead.
• Fixed /translation qualifier that was incorrectly generated for CDS features on protein sequences imported from GenPept or UniProt files.
• Fixed a potential crash when adding or removing enzyme recognition sites in translated sequences using Silent Mutation tools.
• Fixed several display options that remained selectable even when they had no effect given other unselected settings.
• Fixed a delay before the matching codon in the generic translation was shown in bold.
• Fixed a crash cancelling the activation dialog on Linux.
• Fixed blurry, low-resolution graphics appearing on high-DPI displays at startup.
• Fixed Import Custom Features failing to import features.
• Fixed the file extension not updating when switching formats in the export dialog on macOS.
• Fixed spurious /label qualifiers and truncated feature names when exporting in GenBank format.
• Fixed the Edit DNA Ends dialog flickering and minimizing unexpectedly on Linux.
• Fixed a spurious warning when hovering over the enzymes view while SnapGene was not focused.
• Fixed a crash caused by a background thread being shut down too early.
• Fixed a crash when a content pane was accessed after it had been closed.
• Fixed the table header background not updating correctly in split view.
• Fixed Golden Gate Assembly clipping features that overlap Type IIS 5' overhangs.
• Fixed positions in range-type qualifiers not being handled correctly, including complemented locations on the reverse strand and single-base locations.
• Fixed a crash and a duplicate tab opening when double-clicking rows in the archive table.
• Fixed a single invalid primer preventing valid primers from being imported into the primer database.
• Fixed CRISPR guide scoring being offered for Cas9 NGG targets that are not 20 bases.
• Fixed the Database Primers tab not always remaining open after changes.
• Fixed being unable to add labels in All Primers when no labels existed yet.
• Fixed dropdown menus being available in DNA/RNA archives when no row was selected.
• Fixed an issue where side-by-side split view could make the window too wide for the screen.
• Fixed a contig assembly file being created even when the assembly failed.
• Fixed the contig assembly folder not respecting the user-specified name.
• Fixed selections referring to CRISPR guides as "crispr".
• Fixed opening the primer database tab disabling undo and redo in other files.

• Fixed an issue where newly created files could fail to show the unsaved changes indicator
• Right-click context menus are now working for primer databases
• Fixed an issue where select all actions were not selecting CRISPR table contents
• Fixed an issue where CRISPR scoring was showing offline for users without cloud access
• Fixed an issue where checkboxes were not showing for users on MacOS Golden Gate
• Annotating from a newly created or edited primer no longer causes binding site numbers to disappear
• The primer database import dialog no longer unselects valid primers when filters are used
• Tooltip no longer flashes when resizing a column header on Windows 
• Clicking a macOS Dock menu file item now correctly activates its tab in the project window
• Dragging a project window tab no longer flickers a preview image in the centre of the screen
• Restoring multiple files from the macOS Dock now works correctly
• Fixed an issue where certain dropdown menus were inaccessible for MacOS Golden Gate users
• Fixed crash on macOS when painting alignment view features
• Fixed a crash on macOS that could occur during shutdown
• Expanded fragment view now correctly shows end fragments for linear sequences