Home » Release Notes » 5.0.0

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.
  • Fixed an issue in which previously computed information about alignment to a reference DNA sequence could be lost when an aligned sequence was unchecked in the list before saving the file.
  • Disabled "Edit → Delete" when the cursor is placed while viewing a multiple alignment.
  • Prevented an issue that sometimes could occur when restoring an original alignment to a reference DNA sequence.
  • Fixed issues with undoing the realignment of sequences to a reference DNA sequence.
  • Improved the behavior when replacing feature names in a collection.