SnapGene 6.2 Feature Overview

Watch an overview of new features in SnapGene 6.2

RNA Secondary Structure Enhancements

Suboptimal RNA secondary structures are now shown. All structures can be recalculated using adjusted Tm and other settings. Visualization and selection capabilities have been enhanced, including the ability to display and make sequence selections that are synced across all views. Coordinates and 5' / 3' end labels can optionally be displayed. See View Predicted RNA Secondary Structure for more information.

Golden Gate Assembly Enhancements

Various enhancements to the Golden Gate cloning dialogs include a ligation fidelity matrix for assessing overall reaction fidelity, it is now possible to adjust overhangs for manually designed primers. There is also a new option to cut the vector with any enzymes (not just Type IIS enzymes), as well as an updated settings dialog with easy access to recommended enzymes.

Primer Enhancements

You can now adjust the hybridization region for all PCR cloning simulations (e.g. PCR, Golden Gate, Gibson, In Fusion, etc.). When using automatic primer design the hybridized region will be configured automatically, ensuring miscellaneous features are not transferred to the product when a 5’ primer extension by chance partially hybridizes to the template.

Protein Properties Enhancements

Copy or export the properties and amino acid data for full protein sequences or selected regions in text or spreadsheet (*.csv / *.tsv) formats. Individual properties can also be copied directly from the view.

Modernized toolbar, application, and document icons

SnapGene now uses modernized icons in the top toolbar. The application icon and file icons have also been updated.

SnapGene 6.1 Feature Overview

Watch an overview of new features in SnapGene 6.1

Golden Gate Assembly

Confidently simulate Golden Gate Assembly with a new tool which can automatically design primers and overhangs for Golden Gate, optimizing the reaction fidelity to maximize the likelihood of success.

► Watch to learn how to simulate Golden Gate Assembly in SnapGene

RNA Secondary Structure

Visualize how your single stranded RNA sequences will fold with a new Secondary Structure view which displays the optimal structure as calculated by the ViennaRNA Package.

► Watch to learn how to view your secondary structure

Dark Mode

The SnapGene user interface now supports dark mode and by default will match your Dark or Light mode operating system setting.

Export Options

Customize how content is exported to GenBank including LOCUS field identifier feature export options using the new Export panel in Preferences.

Support for Apple Silicon

SnapGene now runs natively on Apple computers with M1 silicon chips.

SnapGene 6.0 Feature Overview

Watch an overview of new features in SnapGene 6.0

Silent Mutation to Add or Remove Enzyme Sites

Restriction enzyme sites can now be automatically added or removed from a coding sequence by silent mutation.

Support for Custom Feature Types

The set of available feature types can now be extended to include custom types (non-GenBank), and default feature colors can be changed.

Agarose Gel Files

Agarose gel simulations can now be saved as .gel files, allowing gels to be viewed and edited later or shared with others.

Feature Annotation in Pairwise and Multiple Alignments

Editable features are now fully supported in both pairwise and multiple sequence alignments, with the ability to add, edit, and search from either the Alignment view or the new Features view.

Cloning Simulation Enhancements

New flexibility in cloning simulation dialogs enables fragments to be added, removed, or re-ordered within the cloning interface. Vectors can now be flipped when simulating restriction cloning, Gibson Assembly, In-Fusion Cloning, and NEBuilder HiFi Assembly.

SnapGene 5.3 Feature Overview

Watch for an overview of the new features in SnapGene 5.3

View Features in Multiple Sequence Alignments

Features in the input sequences are carried through to the alignment, allowing you to visualize aligned regions in context.

View and Export History in Text Format

History view now supports both the traditional Maps format and a new Text format.

RNA Sequence Files

The new .rna file format allows you to create, view, and edit RNA sequences.

New ‘All Files’ Area in Collections

Organize all of your DNA, RNA, and protein files within a single list or folder tree in a Collection, and add new folders across the different areas in a single step.

View Sequences in Blocks of 3 or 10 Residues

New layout options allow sequences to be displayed with gaps every 3rd or 10th base.

Fill In Annealed Oligos

Overlap two oligos, and then convert to double-stranded DNA in a single step by filling in the overhangs.

Primers with 3' Overhangs

A DNA sequence can now be annotated with primers that anneal at the 5’ end but not the 3’ end.

Wrapped View for Chromatogram Files

Display and print a chromatogram in multi-line format to view the trace more efficiently.

Improved Geneious Format Conversion

Individual .geneious protein and nucleotide sequences, including features, primers, and alignments, are now imported more reliably with richer information.

SnapGene 5.2 Feature Overview

Watch for an overview of the new features in SnapGene 5.2

GC Content Display

A GC content color or line plot can now be displayed in Map view, and bases can be colored by GC or AT in Sequence view.

Find Similar DNA Sequences

When searching for DNA sequences, imperfect matches containing gaps or mismatched bases can be found, and search performance has been optimized.

Supercoiled DNA Migration

When simulating agarose gels, the migration of uncut circular sequences can be visualized, and supercoiled MW markers can be used.

ssDNA Sequences

A single-stranded DNA (ssDNA) sequence can now be created or imported, with support for feature annotation and sequence manipulations.

Optimized History View

When editing sequences, the history is compressed to allow efficient storage as well as Undo for large sequences.

Additional Protein Feature Types

The set of supported protein feature types has been extended, including support for the misc_feature type.

Sequencher File Import

Sequencher files can now be imported into a SnapGene collection.

Better Linear Maps

Enzyme sites and other annotations in a linear map are now allowed to overlap, thereby reducing map height while preserving legibility.

Optional Split View

A DNA or protein sequence window can be split to show two different views, or two versions of the same view.

Enzyme Visibility Controls

Like features and primers, individual enzymes can now be shown or hidden using check boxes.

Links Between Collection Areas

When a SnapGene collection stores related files in the DNA Files, Protein Files, and Miscellaneous Files areas.

Flexible Choice of Reference Type

When adding references to the Description Panel, a variety of reference types are now available.

Adjustable Threshold for Feature Detection

When importing features from another SnapGene file or detecting common features, the match threshold can be adjusted between 80-100%.

Batch Edits in Collections

A SnapGene collection now supports batch edits of multiple files for flipping sequences, importing features or primers, detecting features or primers, performing BLAST searches, and specifying entries in the Description Panel.

Optional Stripes for “A” Traces

In a sequence trace file, the “A” trace can be displayed with stripes to support researchers with color vision disabilities.

Pre-defined “Type IIS Enzymes” Set

Type IIS enzymes, which are used for Golden Gate assembly, can be displayed using a pre-defined enzyme set.

Pairwise Alignment

Pairs of DNA or protein sequences can be analyzed by local, global, or semi-global alignment.

Import from Ensembl

Gene or transcript data from the Ensembl genome browser can now be imported directly into SnapGene.

Directional TOPO® Cloning

A new interface simulates directional TOPO® cloning into topoisomerase-activated vectors.

Flexible Alignment to a Reference

The interface for aligning to a reference DNA sequence has been enhanced. Controls for various display options are more intuitive, and alignment can be restricted to a designated strand or region of the reference sequence.

Draggable Nonaligned Ends

For a sequence that has been partially aligned to a reference DNA sequence, the nonaligned end portions can now be dragged out and visualized.

Anza™ Enzymes

The Anza™ enzyme system from Thermo Fisher (Invitrogen) has been incorporated into SnapGene’s enzyme database.

Customizable Background Color

The background color for the SnapGene interface can be changed.

Visibility Controls for Feature Types

Features can be shown or hidden based on feature type.

New Options for Amino Acids

Amino acids in a translated feature can be set to lowercase, and a stretch of amino acids can be copied in 3-letter format.

Codon Frequencies Calculator

A codon frequencies table can be generated for one or more translated features.

DNA-to-Protein Alignment Conversion

A selected region of a DNA alignment can be translated to generate the corresponding protein alignment.

Intron Annotation for an Aligned cDNA

When a cDNA is aligned to a reference genomic DNA sequence, the cDNA can be used to create a feature in which gaps are annotated as introns.

Extended Selection Endpoints in Maps

Selections are now marked with extended lines, which clarify the selection endpoints and also enhance visibility for small selections.