SnapGene 7.2.0

What's new in this version:

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