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Changes in version 5.2 (Oct 13, 2020)
New Functionality:
- Enabled visualization of GC content as a color plot in Map view or base colors in
Sequence view.
(Requested by Michael Brooks, Max Garwood, Robb Stankey and others) - Added support for finding similar DNA sequences with mismatches or indels compared to the
search query.
(Requested by multiple users) - Added support for simulating the migration of supercoiled DNA molecules in agarose gels
using TBE, TAE or SB buffer.
(Requested by multiple users) - Added support for single-stranded DNA (ssDNA) sequences.
(Requested by John O'Brien and others) - Enabled import of Sequencher project files (*.spf).
(Requested by May Cindhuchao, Heather McFarlane, and Usua Oyarbide) - Enabled "Undo" for edits in large sequences.
- Added DNA ladders from DyneBio.
(Requested by Dae-Geun Song) - Added supercoiled MW markers from ELPIS BIOTECH and New England Biolabs.
- Added BsmBI-v2 to the list of enzymes available from New England BioLabs.
- Added fields for username and email address in the license registration dialog.
Enhancements:
- Optimized storage of history for the following operations: Change Methylation,
Change Transformation Strain, Set Origin,
Flip, Insert/Delete/Replace, Linearize, Circularize.
(Requested by Dan Lysko, and by others who complained about large files) - Updated the supported protein feature types by adding new types (NonStdRes, Protein,
Precursor, SecStr, Het, CDS, gene, misc_feature, unsure, variation),
promoting Region subtypes to types, and adding new Site and Bond subtypes.
(Requested by Sanofi) - Added a note in Features view to indicate the presence of internal stop codons in a
translated feature.
(Inspired by Tom Hamer) - Enhanced the Preferences tools to allow more flexible default options for displaying ORFs.
(Requesed by Caroline Reiss) - Enabled carrying over feature qualifiers when creating a protein sequence using
"Make Protein" or "Reverse Translate".
(Requested by Katherine Geromini) - Added the option to merge segments when using "Make Protein" on a multi-segment DNA feature.
- Added a "Hide noncutters" check box in the Choose Enzymes dialog.
(Inspired by Bruce Lahn) - Enabled importing features from any supported file type when using "Import Features
from a SnapGene File".
(Requested by Greg Perry) - Enabled more flexible batch conversion of chromatogram traces to other formats.
(Requested by Arthur Fridman) - Improved search performance for large DNA sequences.
- Configured the minimap to show both scrolled areas when two copies of Sequence view are visible.
- Updated the format of the Preferences dialog, and added an "Agarose Gels" tab.
- Added the option to designate a new collection as the Main Collection.
- Enabled saving imported online sequences directly to a collection.
- Added shortcuts in a collection Overview for navigating to the DNA Files, Protein Files, or Miscellaneous Files sections.
- Enabled symbols to be entered in search queries when searching SnapGene Online Sequences.
- Increased the size of the length indicator in the map label at the "Small" font size.
- Consolidated all Fisher MW Markers for agarose gels in the Fisher Scientific set.
- Configured the Nonredundant Commercial enzyme set to include similar enzymes that differ by methylation sensitivity.
- Configured SnapGene to show the Launch dialog on macOS when the SnapGene icon in the Dock is clicked, if no SnapGene windows are open.
- Changed the icon for enabling interrupted circle format for a linear DNA sequence in Map view.
- Configured the "Export Map" and "Export History" options to be always enabled.
- Improved the wording of various menu options and dialogs to provide greater clarity and consistency.
- Added a message informing the user that files can be dragged into the list when using Align Multiple Sequences.
Fixes:
- Fixed an issue that prevented cloning dialogs from allowing the use of hidden enzymes.
(Reported by Mily Ron) - Corrected an issue in "Protein Search" whereby terminal stop codons were not included in
the search query.
(Reported by Mike Xie) - Ensured that edits in an alignment window do not cause inappropriate scrolling.
(Reported by Beth Lawrence) - Corrected an issue that could prevent alignment of a high-quality sequence trace.
(Reported by Jessie Saul) - Ensured that the "Find" control in the Enzymes view chooser always shows a message to indicate if the enzyme is not in the chosen set.
- Corrected an issue in which U's in overhangs resulting from linearizing were not preserved.
- Configured "Select All" in the trace viewer context menu to actually select all.
- Ensured that History view reflects changes after editing DNA ends.
- Ensured that case changes in the "Find" entry field are preserved when the search is executed.
- Ensured that imported RNA alignments are converted to DNA rather than protein alignments.
- Corrected the license inactivity countdown to displays seconds rather than milliseconds.
- Ensured that the "Accession Number:" label remains next to its entry field in the collection Search dialog.
- Ensured that a "Sequence Name" search in the Protein Files area of a collection also searches the map labels and aliases.
- Corrected an issue that resulted in alignment and collection windows not showing unsaved changes in the title bar on Windows and Linux.
- Ensured more consistent sorting of enzymes in the Choose Enzymes dialog.
- Streamlined the substitution matrix options presented when computing pairwise alignments.
- Ensured that open alignments can be used as profiles when computing new alignments.
- Corrected an issue that could result in the "Kind" column disappearing when viewing a collection.
- Ensured that crisp screenshots are shown when detecting updates.
- Improved import of the full publication date from PubMed.
- Made various stability fixes.