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Changes in version 5.0 (Sep 23, 2019)
- 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,
(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
(Requested by Walid Azar)
- Added a control for exporting selected files in a collection as a list in PDF or
(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".
- 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.
- 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.