SnapGene Version 4.3.0

SnapGene 4.3.0 was released on February 05, 2019.

Overview

Version 4.3 adds multiple new features including contig assembly, more flexible alignment tools, support for nicking endonucleases, and support for point features.

Contig Assembly

Linear or circular contigs can be assembled de novo from overlapping sequences or Sanger sequence traces.

Flexible Alignments

Sequences to be aligned can now be imported in various ways. A portion of a multiple alignment can be extracted to generate a new multiple alignment, or an existing multiple alignment can be edited to add or remove alignments generated by different algorithms.

Nicking Enzymes

Nicking endonucleases can be displayed. When a selection spans from an end of a linear sequence to a nicking endonuclease site, that single-stranded region can be removed by pressing Delete.

Point Features

Zero-length point features are now supported for DNA sequences, and are recognized when importing files from GenBank, MacVector, or Gene Construction Kit.

Enzyme Site Highlighting

Commonly used enzyme sites can be highlighted in gold for quick identification.

Alignment Consensus Enhancements

Consensus sequences for multiple alignments have an improved format, and can now be copied or exported.

Stored Edits for Alignment to a Reference Sequence

By popular demand, when an alignment to a reference DNA sequence is edited by adjusting the endpoints of the aligned sequences, those edits are preserved and restored.

Feature Import from Other File Formats

Features can be imported into a DNA sequence from BED, GFF3, or GTF formats.

Import from UniProt

Protein sequence records can be imported from the UniProt database.

Import of Genome Compiler Projects

Genome Compiler project files (.gcproj) can now be opened directly in SnapGene. For construction project files, the construction histories are captured in History view.

Primer Addition Dates

When a primer is added to a file, the date is recorded. Primers can be sorted by Date Added.

Reading and Writing Alignment File Formats

SnapGene can import alignments to a reference sequence in SAM/BAM and Vector NTI® .cep formats, and can export alignments to a reference sequence in SAM/BAM formats.

New Functionality

• Added support for de novo contig assembly from overlapping sequences or Sanger sequence traces.
  (Requested by multiple customers)
• Added an option to create a sub-alignment by selecting and then realigning part of a multiple sequence alignment.
• Preserved custom numbering of aligned sequences when computing multiple sequence alignments.
• Added options to add an alignment using a different algorithm or to remove an existing alignment in a multiple sequence alignment window.
• Provided support for nicking endonucleases.
  (Requested by Luay Joudeh, Rufeng Wang, Sarah Darling, Ivan Mikaelian, John Kung, Dustin Rubinstein, Di Yu, and others)
• Added the ability to remove a single-stranded region from a linear sequence by selecting from a DNA end to a nicking endonuclease site and pressing Delete.
• Enabled deletion of a restriction fragment after selection from the end of a linear sequence to a restriction site.
• Added support for point features, including import of point features from other file formats.
  (Requested by Allan Drummond, Tyler Bradshaw, and Michele McConn)
• Added the ability to highlight one or more enzyme sites.
  (Requested by Dan Strongin and Brigitte Lavoie)
• Added support for copying or exporting part or all of the consensus sequence from a multiple sequence alignment.
  (Requested by Elaine Joseph, Emily Isgur, Casey Keyes, and Shannon Phan)
• Improved the consensus format in multiple sequence alignments to use light gray X's or N's where consensus is lacking.
• Enabled the import of copied and open sequences, as well as import from NCBI and UniProt, when computing multiple sequence alignments.
• Enabled recomputing of an alignment to a reference DNA sequence using the "Aligned Sequences" button menu.
• Configured manual trimming of sequences aligned to a reference DNA sequence to be both undoable and saved, and set the trimming stringency to be undoable and saved on a per-file basis.
  (Requested by George Ghanim, Icon Genetics, Dave Bailey, Aaron Alt, Mily Ron, and Lennert Janssen)
• Ensured that small edits to a sequence aligned to a reference DNA sequence result in the alignment being updated rather than recomputed from scratch.
• Converted the view of alignments to a reference DNA sequence to a display parameter that is restored the next time a file is opened.
• Enabled the import of features from BED, GFF3, and GTF formats.
  (Requested by Alison Pidoux, Eddy Risseeuw, Maria Gonzalez, Jonathan Woodsmith, Erin Boyle Anderson, Yun Wu, Patricia Baker, Amyris, Yaara Yoren, David Kovalic, and Joe Georgeson)
• Added a dedicated dialog for import of protein sequences from UniProt.
• Enabled SnapGene to track the dates when primers are added to a sequence, and to sort primers by Date Added in Primers view.
  (Suggested by Tim Rand and Steven Erickson)
• Enabled SnapGene to open Vector NTI .cep contig assemblies directly.
  (Requested by Wouter Pos)
• Enabled SnapGene to open SAM / BAM contig assemblies directly.
• Enabled SnapGene to import from and export to SAM/BAM alignment formats.
  (Requested by Zhonggang Hou)
• Enabled SnapGene to open GCG (Genetics Computer Group) encoded DNA and protein sequences and archives directly.
• Allowed sequences in SAM / BAM files to be imported for alignment to a reference DNA sequence.
• Enabled GCG and PIR / NBRF content to be pasted into the New DNA / Protein file dialogs.
• Added an importer for Genome Compiler project and cloning project files.
  (Requested by Doug Daniels and Martin Schneider)
• Enabled the import of open sequence files for aligning to a reference DNA sequence.
• Added buttons for moving selected sequences to the top or bottom of the list when first specifying sequences for a multiple sequence alignment.
• Added the ability to copy DNA selections as RNA by holding the Opt/Alt key.
  (Requested by Karl Brune)
• Added New England Biolab's "λ DNA – Mono Cut Mix" ladder.
  (Requested by Shari Carmon)

Enhancements

• Added the ability to use Shift + Enter to navigate to previous search results.
  (Suggested by Karl Brune)
• Increased flexibility when exporting multiple sequences from a collection.
  (Requested by Iris Dotan and Frank Thieme)
• Ensured that when saving a collection, if the chosen collection name already exists, an option is provided to choose an alternative name instead of simply appending a number at the end.
  (Requested by Carles Alvarez)
• Added the ability to adjust the default start codons for newly entered and imported DNA sequences.
  (Requested by Tim Barnett)
• Dramatically sped up opening of large FASTA archives.
  (Reported by Sierra Dargan)
• Enabled the labeling of all or no lanes containing MW markers as "MW" when simulating an agarose gel.
  (Requested by Brianna Bibel)
• Added "Go To..." to the Find bar menu.
  (Requested by Charles Zhu)
• Made numerous significant optimizations
  (e.g., when opening, importing, or interacting with sequences).
• Made various textual, color, icon, and visual alignment enhancements.
• Improved progress indicators when computing multiple sequence alignments.
• Provided the option of computing a faster MUSCLE alignment if the full computation would take a long time.
• Improved residue tooltips in multiple sequence alignments.
• Enabled the default sorting option to be specified for a collection.
• Added tooltips to various controls to indicate the associated keyboard shortcuts.
• Added the ability to insert symbols into the name of an aligned sequence.
• Preserved custom map labels when importing sequences for alignment.
• Provided the option to replace the embedded display options with preferred display options when importing from Addgene or SnapGene.
• Configured the import of multi-sequence archives to generate SnapGene collections, thereby allowing for quick browsing and searching of the converted archives.
  (Requested by Tijs van den Bosch)
• Improved security by using https for all network communication.
• Ensured that localized dates are shown using the preferred format.
• Added convenient controls for extending the selection in the Select Range dialog.
• Improved the workflow when batch converting files.
• Ensured that when the top toolbar is hidden, formatting controls are still available in the Description Panel.
• Switched to the https secure network protocol for all forms of network communication.
• Added a keyboard shortcut for "Show Alignments".

Fixes

• Improved the import of GenPept files when computing a multiple sequence alignment.
  (Reported by Junwei Ji)
• Prevented a hang and eventual crash that could occur if several features are in frame with each other in a circular sequence.
  (Reported by Pedro Olivares)
• Improved the Cut button icon clarity using the small size on Retina displays.
  (Reported by Pedro Matos)
• Improved MW accuracy for ORFs and translated features containing ambiguous amino acids, as well as Properties view in protein windows and Primers view in DNA windows.
  (Reported by Andriy Volkov)
• Fixed various issues with the buttons for flipping inserts in the Gibson Assembly and In-Fusion Cloning dialogs.
  (Reported by Andreas Kjaer)
• Improved stability when editing a collection's code number format.
  (Reported by Viktoria Lytvyn)
• Improved the decoding of XML-formatted content (e.g., DS Gene files) on Windows.
  (Reported by Mary Russell)
• Ensured visibility of small feature segments in a map.
  (Reported by Cas Simons)
• Fixed a regression to allow pasting of a fragment into an Insert tab of Actions > Restriction and Insertion Cloning > Insert Fragment(s).
  (Reported by Rishikesh Ghogare)
• Enhanced the stability of the multiple sequence alignment consensus display.
  (Reported by Luca Jovine)
• Fixed an issue with the "Save As" keyboard shortcut on Windows.
  (Reported by Adi Millman)
• Improved stability when aligning very low quality sequences.
  (Reported by Chris Craddock)
• Ensured that AanI will be displayed in the list box in the Simulate Agarose Gel dialog.
  (Reported by Wulf-Dirk Leuschner)
• Improved feature segment borders in Sequence view.
  (Suggested by Carles Recasens Alvarez)
• Improved the opening of Geneious files to support annotated sequencing data.
  (Requested by Hai Ying Yuan)
• Ensured that the application does not get stuck when renaming a primer in an Action dialog.
  (Reported by Jordan Voisine)
• Prevented the "Move" controls for aligned sequences from being disabled while viewing an alignment to a reference DNA sequence.
  (Reported by Masa Esaki)
• Fixed an issue with importing some accession numbers from NCBI.
  (Reported by Ruanbao Zhou)
• Prevented the mouse indicator from being erroneously shown outside the trimmed portion of an aligned sequence.
• Improved the behavior of the top toolbar when working with multiple sequence alignments.
• Added "Preferences" to the launch dialog Help button menu on Linux.
• Allowed for a BOM at the beginning of a primer list when importing from a file.
• Prevented MUSCLE from outputting partial results.
• Prevented menu commands from being erroneously enabled after canceling out an export dialog.
• Disabled the "Set as Default Parameters" button when it will have no effect in the Align Multiple DNA/Protein Sequences dialogs.
• Enabled top toolbar menu commands listed under View → Toolbars while viewing multiple sequence alignments.
• Corrected the ruler numbering when using the Edit DNA Ends and Add/Edit Primer dialogs.
• Made it easier to double-click to select a word in a name field.
• Configured the New Protein File dialog to accept pasted '?' characters and convert them to X's.
• Fixed an issue with showing an enzyme set saved to a local file in a cloning dialog.
• Enabled a trimming handle in an alignment to a reference DNA sequence to be clicked and dragged directly, without first assigning focus to that interface element.
• Improved the Tab responses in multiple sequence alignment dialogs.
• Prevented the logging out of macOS from being thwarted by open SnapGene files.
• Disabled various commands such as Actions → PCR when a modal dialog is shown.
• Removed code numbers warnings shown in the collection window list after the issues have been resolved using the Description Panel.
• Fixed invisible checkmarks for items in menus on Windows and Linux.
• Ensured that the Order button is hidden when toggling the top toolbar with rich text controls visible.
• Fixed the Tools menu in the Launch window to hide nonessential items on Windows and Linux.
  (Reported by Debra Hansen)
• Improved the painting of bottom strand cleavage triangles when they overlap features in Sequence view.
• Ensured that when features are hidden by default in the DNA tab of Preferences, they are still visible by default in the Browse Common Features dialog.
• Prevented a crash that could occur when clicking widgets in the Edit Code Number Format dialog.
• Enabled the display of unknown enzymes in History view.
• Improved stability when quitting the application while a tooltip is visible.
• Configured Sequence view to scroll automatically to a selected primer-primer fragment.
• Ensured that Undo and Redo commands are cleared after a document is closed.
• Enabled "Paste Reverse Complement" when a DNA search or primer sequence control has focus.
• Enabled the proper action of "Export Selected File" when viewing miscellaneous files in a collection.
• Corrected a regression to show an error message if the Make Protein command is invoked when there is no selection.
• Made various stability enhancements.
• Improved the selection bar display when multiple protein features of different types are selected.
• Ensured that a file is not marked as unsaved after adding or removing enzymes from the chosen set.
• Fixed an issue with showing history colors in History view when selecting consecutive operations.
• Improved the highlighting of non-aligned primer bases in PCR product history colors.
• Ensured that History view correctly displays the number of times an enzyme cut an ancestor sequence.
• Improved rendering of the ruler for an aligned FASTQ read when aligning to a reference DNA sequence.
• Ensured that various "Export" context menu actions do not result in the dialog instantly disappearing on macOS.
• Removed the inappropriate watermark option from the Options dialog when exporting a gel image.
• Prevented unexpected Undo/Redo behavior after adding files to a collection.