Changes in version 5.0 (Sep 23, 2019)

New Functionality:

• Added tools for pairwise alignment of DNA and protein sequences.
  (Requested by many customers)
• Added interfaces for simulating directional and blunt TOPO® cloning.
  (Requested by many customers)
• Provided support for customizing the background window color.
• Added the ability to drag out and view non-aligned ends of aligned sequences.
  (Requested by just about everyone)
• Added the ability to display feature translations in lowercase.
  (Requested by Peter Drain)
• Enabled alignments to be constrained to a designated strand or region of the reference DNA sequence.
  (Requested by Christel Aebischer and others)
• Added the ability to import sequences directly from Ensembl.
  (Requested by Jaeho Ryu, Elena Fujiwara, and others)
• Enabled the calculation and saving of codon frequencies for one or more translated features.
  (Requested by Craig VanDolleweerd and Jeanie Lin)
• Enabled feature visibility to be toggled by feature type.
  (Requested by Di Xia and Lee-Chung Lin)
• Added the option to trim low-quality ends when importing sequence traces for contig assembly or multiple sequence alignment.
• Enabled an aligned cDNA to be used to annotate a feature with exons and introns.
  (Requested by Rob Steele and Peishan Yi)
• Added support for opening DNASIS files.
  (Requested emotionally by Jim Galen)
• Enhanced BLAST support to provide all five options (blastn, blastx, tblastx, blastp, and tblastn).
  (Requested by Inbar Plaschkes)
• Updated the "Aligned Sequences" menu when viewing an alignment to a reference sequence, and added the following new commands: • Duplicate Selected Sequence(s) in New Window(s) • Remove All Sequences • Show/Hide Quality Data for Sequence Traces
• Added a control in Preferences to enable quality data for sequence traces to be shown by default when aligning to a reference DNA sequence.
• Enabled a selected portion of a multiple DNA alignment to be converted to a multiple protein alignment.
  (Requested by Walid Azar)
• Added a control for exporting selected files in a collection as a list in PDF or tab-separated format.
  (Requested by David Murray)
• Added a "Choose DNA Sequences..." button to the Simulate Agarose Gel dialog, as a shortcut for configuring multiple lanes.
  (Requested by Dhaval Bhatt)
• Enabled amino acid sequences to be copied as either 1- or 3-letter amino acid codes.
  (Requested by Moo-Hyung Lee)
• Enabled the copying of selections that span multiple lines in pairwise or multiple alignment windows.
• Added the New England Biolabs "TriDye™ Ultra Low Range DNA Ladder".

Enhancements:

• Calculated the total length of the segments for a feature with gaps, with this information now displayed in Features view, feature dialogs, and feature tooltips.
  (Requested by Di Xia)
• Reduced the width of the "Code Number" column in the collection interface by using an icon.
  (Requested by Carles Alvarez)
• Added the option to preserve a feature translation by adjusting its reading frame when exiting the Edit Feature dialog.
  (Inspired by Wulf-Dirk Leuschner)
• Added an option in Preferences to display the MW of a selection in a protein file in Daltons.
  (Requested by Eric Fang)
• Added a notification if some of the input sequences were not included when assembling contigs.
  (Requested by CLS)
• Added a keyboard shortcut for importing primers from a list.
  (Requested by Benjamin Weinberg)
• Relaxed a restriction that prohibited < and > characters in primer names.
  (Requested by Tomoyuki Kosaka)
• Improved the detection of T7 promoter features.
  (Reported by Kevin McGowan)
• Improved import from NCBI to tolerate regions in which the left and right endpoints are swapped, and to recognize "c" as denoting the reverse complement.
  (Requested by Rachel Delston)
• Added support for new genetic codes.
  (Requested by Dilbag Multani)
• Improved the algorithm for aligning to a reference DNA sequence.
  (Requested by Leonid V.)
• Improved the import of features from BED and GTF files generated by geneXplain.
  (Requested by John Bass)
• Enhanced the Vector NTI® database importer to recognize separators.
  (Requested by Sanofi)
• Provided the version numbers of alignment programs (e.g., MUSCLE) in the user interface.
• Improved the visibility of selections and their endpoints in maps by including lines that extend below the DNA line.
• Enhanced the "Edit MW Markers List" dialog to support display of MW markers by supplier, and to enable one-step selection of all MW markers from a supplier.
• Dramatically improved scrolling performance in Features view for sequences with many features.
• Added commands to the Enzymes and Primers menus for pulling up the corresponding tabs in Preferences.
• Enhanced Properties view in protein windows to list both average and monoisotopic molecular weights.
• Made the alignment dialogs modeless to enable switching to other SnapGene windows.
• Improved the visibility of a Consensus selection in a multiple alignment window by extending blue lines down from each end of the selection.
• Made extensive optimizations to speed up application launch and use in general.
• Switched from WebKit to QTextEdit for rich text controls.
• Improved the support for links in feature qualifiers and in Description Panel fields.
• Enhanced the TA and GC Cloning dialogs to allow simple issues (e.g., lack of 5' terminal phosphates or overhangs) to be addressed by clicking a button.
• Improved the controls for toggling the visibility of sequences aligned to a reference sequence.
• Improved the controls for switching between showing an aligned sequence trace as double-stranded DNA or a chromatogram.
• Added a warning that only Clustal Omega can preserve internal stop codons when computing a multiple sequence alignment.
• Enabled a Main Collection to be specified if necessary when using "Save to Main Collection".
• Added "List View" and "Folder View" commands to the View menu when browsing a collection.
• Moved the "Design Synthetic Construct" and "Order Construct" commands to the Tools menu.
• Consolidated the default font size settings for all file types (DNA, protein, alignments), and added support for the default font size for alignments.
• Improved the discoverability of using Opt/Alt to see all four base heights when mousing over a peak in a sequence trace.
• Added a "Manage Codon Usage Tables" command to the Tools menu, because previously this option was only accessible from the "Codon Usage Tables" dialog.
• Ensured that rich formatting (bold, italic, underline, super- and subscripts) are visible in Features view even when full descriptions are not shown.
• Added "GC Content" values to the DNA Calculations window.
• Enabled export of gel images, maps, and histories to the EMF vector format on macOS for import into Microsoft Office products.
• Added "Show/Hide All Features" commands to the Features menu.
• Added "Show/Hide All Primers" commands to the Primers menu.
• Ensured that when importing from NCBI, the LOCUS field is used as the default file name.
• Enhanced the logic so that when importing from the SnapGene online database, a perfect match to the query is automatically selected even if it is not the first match listed alphabetically.
• Added the ability to transfer a selection between the Consensus and an aligned sequence in a multiple alignment window by using Cmd/Alt + click.
• Added keyboard shortcuts for the "Flip Sequence" and "Set Origin" commands.
  (Requested by Michael Lemieux)
• Enhanced the flexibility of a protein search to strip a terminal stop codon from the query if appropriate.
• Improved support for copying maps, history, and agarose gels and pasting in vector format into Microsoft Office on macOS.
• Added support for the following qualifiers with the following feature types. exon & intron: /trans_spicing; misc_recomb: /recombination_class; rep_origin: /function; source: /metagenome_source; tRNA: /operon.
• Improved the options available for the feature qualifiers /recombination_class, /regulatory_class, /db_xref, /gap_type, and /ncRNA_class.
• Added a shortcut for "Set Translation Numbering".
• Improved the layout of enzymes in linear maps.
• Improved the genetic code choice for ORFs and non-feature translations when importing from NCBI and opening GenBank and EMBL files.
• Configured the tool for alignment to a reference DNA sequence so that flipping the reference sequence or resetting the numerical origin preserves the alignments instead of recomputing them.
• Improved the visibility of bands when using MilliporeSigma's DNA Molecular Weight Marker IV and VII.
• Added supplier information for the New England Biolabs BsaI-HF®v2 enzyme.
• Added supplier information for the Thermo Fisher (Invitrogen) Anza™ enzymes.
• Made various textual, color, and other visual enhancements.

Fixes:

• Prevented copied gel images from being clipped when pasting into Microsoft Office.
  (Reported by Christian Probst)
• Fixed an issue with decoding some RTF-encoded content (primer lists, etc.).
  (Reported by Elisabeth Boger)
• Improved detection of T7 promoters and other non-translated features.
  (Reported by Kevin McGowan)
• Ensured that terminal phosphates are never shown at the end of protein sequences.
  (Reported by Karl Brune)
• Enabled closing of the License Agreement dialog by pressing the Escape key.
• Fixed the vanishing "Save As" dialog after importing a file and then choosing "Save" in the top toolbar Save button menu.
• Omitted the background color when printing or saving the EULA.
• Removed various irrelevant disabled menu commands when viewing protein sequence windows.
• Prevented the "Save" command in the top toolbar menu from changing to "Save All" when Opt is pressed.
• Corrected the translation of reverse directional features imported from BED and Genome Compiler files.
• Added a requirement that Insert sequences in the TA and GC cloning dialogs are < 50 kb.
• Corrected various standard plasmids to not include "(linearized)" in the map label.
• Corrected the endpoint modifications for various TOPO® vectors.
• Ensured proper display of super- and subscripts in feature qualifiers and Description Panel fields.
• Enabled the deletion of gaps in multiple sequence alignments.
• Improved stability with Undo after deleting gaps in multiple sequence alignments.
• Enabled "Edit
• > Delete" when a cursor is placed in an alignment window.
• -Fixed various issues with menus updating to reflect the selection in a multiple sequence alignment after using the Select All and Select Range commands.
• Provided an "Edit → Delete Gap Characters" command when only gap characters are selected in an alignment.
• Disabled the Print and Save buttons in the collection interface top toolbar when no content is shown.
• Ensured that the proper position of cleavage arrows is maintained when setting the numerical origin.
• Improved the behavior of the controls in the Select Range dialog.
• Improved the accuracy of primer binding site calculations to ensure that long loops are not inappropriately favored over multiple hybridized stretches.
• Improved support for IP-based licenses, especially when a network connection changes or is slow or is briefly unavailable.
• Enhanced stability during Find operations.
• Prevented an issue with choosing a codon usage table that is incompatible with the currently selected genetic code in the Choose Alternative Codons dialog.
• Ensured that the Edit Codon Usage Table always shows the correct genetic code.
• Fixed an issue with using "Copy ORF Translation" from an ORF context menu when no amino acids are selected.
• Prevented hiding of the top toolbar when switching to Full Screen mode.
• Ensured the proper display of regions aligned downstream of a gap.
• Ensured that right-clicking does not display a context menu if the clicked window is not active.
• Corrected a regression in which recent searches were not listed in the Find control pull-down menus in Features and Primers views.
• Fixed an issue with pliancy and selection in Features view after toggling full descriptions.
• Enhanced stability when opening some CLC Bio files.
• Improved the highlighting of matches when cycling through search results in Features view.
• Improved the "Find" options in the Edit menu when using Enzymes, Features, and Primers views.
• Enabled Enter/Return and Shift-Enter/Return when using "Find ancestor" in History view.
• Improved the conversion of pasted rich content that contains unusual characters in the New DNA/Protein File dialogs.
• Ensured that the "Show/Hide Enzymes" command in the Enzymes menu is enabled only in Map and Sequence views.
• Removed unnecessary warnings about ORFs in Sequence view when displaying the sequence in compact mode.
• Prevented blank commands from being listed under Edit → Find when no items in a collection are selected.
• Corrected an issue with opening MSF files.
• Improved stability when using “Save All” while a collection is visible.
• Prevented blank menu actions under Edit → Find when neither a DNA nor a protein document is visible within a collection.
• Ensured that highlighted mismatches with the reference sequence are always shown in the right color.
• Improved the opening of MSF files.
• Prevented a hang that could occur when attempting to delete a restriction fragment containing a translated feature that spans the numerical origin.
• Corrected an issue that resulted in an empty file list initially being shown in a newly created collection after import from Ensembl.
• Improved stability when using File
• > Save All with many edited files in a collection.