SnapGene Version 7.2.0

SnapGene 7.2.0 was released on March 19, 2024.

Overview

SnapGene 7.2 provides a new visualization of primer homodimer structures and enhancements to file management, allowing tabs to be organized in multiple windows using drag and drop, and improvements to interacting with files in projects.

Calculate Primer Homodimer Structures

Check your primers for self-dimerization by viewing homodimer structures with deltaG values, via the Show Structure buttons in Primers view.  

Draggable File Tabs

Easily group your sequences by dragging file tabs in and out of the window to create multiple tabbed windows.

UX Enhancements for Interacting with Files

Smoother importing and interacting with tabs, files, and folders to address common issues, including enhancing the visibility of the current tab and file name, improved default view settings for chromatograms, drag and drop import into folders, and more.

New Common Features and Agarose Gel Ladders

Can now choose gel ladders from several additional suppliers, and more features have been added to the standard feature database for detection in your sequences.

Features and Enhancements

• Primer homodimers
  • Calculation of primer homodimer structures using the RNAcofold tool from the Vienna RNA package
  • Visualize primer homodimers colored by sequence or confidence
• Tabbed file window enhancements
  • Enabled dragging file tabs in and out of a window
  • Added ability to have multiple windows containing file tabs
  • Tabbed file windows can now exist without a “Project” panel
  • Added current filename to the top toolbar
  • Improved visibility of selected tab
• Enhancements to data management within the Project interface
  • Enabled importing files directly into subfolders
  • Added a drop indicator to signify that files can be imported into Projects by drag and drop
  • Added Expand/Collapse All Folders commands to the file panel actions menu
  • Added an Open File command to the context menu shown when right-clicking a single file in the file panel.
  • Allow opening PDFs in a Project by double-clicking
• Enhancements to chromatogram trace file view settings
  • Adjusted default height so that peaks are not stretched within tabbed windows
  • Display peak information when mousing over quality data
  • Display base highlighting when mousing over trace file sequences
• Updated defaults for In-Fusion cloning to use a 20 bp fragment when there are multiple fragments, as per the updated recommendations from Takara Bio
• Added BioGate ladders (100 bp, 100 bp Plus, and 1 KB) for agarose gel simulations
• Added GeneAll GENESTA ladders (100 bp, 250 bp, and 1 kb) for agarose gel simulations
• Added Hylabs ladders (50 bp, 100 bp, and 1 KB+) for agarose gel simulations
• Updates to Standard common features database
  • Added the Anderson Constitutive promoter set
  • Added alternative Bxb1 integrase and associated sites
  • Added mCyRFP, mScarlet3, StayGold, and mStayGold Fluorescent Protein features
  • Updated Csy4 and human U6 promoter sequences
• Added a ssDNA file to the Sample Project

Additional Changes and Fixes

• Improved performance by avoiding recomputing alignment to a reference DNA sequence when edits are made to the reference or aligned sequences
• Added progress dialog and allow canceling aligning to a reference DNA sequence
• Allow user to specify the quality format if it is ambiguous when importing FASTQ sequencing reads
• Added a side toolbar to the secondary structure view
• Improved the appearance of the Edit DNA Ends dialog when using dark mode
• Removed the option to copy bottom strand bases that were erroneously shown when viewing a protein alignment
• Enable opening non-native files by right-clicking file names in the folder panel
• Expanded the click area in the Choose Enzymes dialog so that options may be selected by clicking on labels to the right of radio buttons
• Improved behavior to avoid unnecessarily showing the main Project window when the “Open files in a separate window by default” preference is enabled
• Translated examples in file search fields
• Fixed a bug whereby assemble contigs was used in an inconsistent default location for results to be stored (Project folder or Collection) depending on the ‘open files in separate windows setting’
• Fixed a crash which occurred when canceling detecting common features on multiple files in a collection
• Fixed a crash which could occur when running file searches in the Project panel
• Fixed a crash that could occur when searching for a region that spans the origin 
• Fixed a bug that made it impossible to resurrect an ancestor after running bulk edits in Collections
• Fixed an error that prevented simulating Gateway cloning using sites that span the numerical origin
• Fixed the enzyme database to show buffer values containing < symbol
• Fixed the alignment of labels in multiple sequence alignments side panel
• Trimmed white space added to the start or end of the email address field
• Enabled the New File pane to be shown on Windows when using a smaller screen
• Ensure features within the amplified region are transferred to the product when simulating PCR using primers that overlap and include internal insertions or replacements.
• Fixed an issue on Windows where amplified fragments disappear in the amplified fragments list depending on which fragment was selected.
• Ensure files double-clicked in the Finder or Windows Explorer are opened full screen if the associated option is checked in Preferences
• Default to the opened project when choosing where to save imported files
• Reduced the minimum width required for file tabs and improved their look and feel when there are a large number of tabs or space is otherwise limited
• Ensure chromatogram quality is printed if it is toggled on
• Improved stability when opening files
• Corrected the uracil count when using Show RNA Calculations
• Added a progress indicator and allow canceling aligning to a reference if it is taking a long time
• Removed “Show Structure” buttons from the Import Primers dialog
• Ensure recently closed tabs are opened in the current window and not a separate window even if the “Open files in separate windows by default” preference is checked
• Fixed an issue where the Golden Gate Cloning dialog could change when accepting out of the adjust overhangs dialog if only one option is available
• Ensure the vector's numerical origin is restored in the assembled product if the vector is digested directly
• Improved performance when working with many tabs
• Fixed an issue with importing files into a project by dropping them on a selected folder
• Ensure vector features are transferred to the product when inserting a restriction fragment
• Fixed an issue that could prevent simulating inserting a restriction fragment
• Optimized performance when detecting sequence topology when creating new files, adding common features, and refining feature colors during import of non-native files
• Implemented new algorithms for searching and indexing sequences, which replace the MICA algorithm, and optimized their performance for core molecular biology use cases
• Reduced file size for newly created and edited files