User Guides

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SnapGene User Guide

Installation
- Download, Install and Register SnapGene
- Adjust the Configuration
- Command Line: Installation and Activation
- Manage A SnapGene Subscription or Permanent License
- Cancel a Recurring Subscription License
- Unregister the Computer You Are Using
- Unregister a Computer Remotely
- Reactivate a Blacklisted Computer
- Set Up or Manage a Shared License Server
Preferences
- Open Full Screen Windows By Default
- Hide or Show the Description Panel By Default
- Show the Launch Window on macOS
- Configure Dark Mode and Background Color
- Set the Background Color (SnapGene 6.0 and earlier)
- Set the Default Font Size for New Files
- Set the Default Transformation Strain
- Set When SnapGene Checks for Updates
- Choose if SnapGene Sends Anonymous Statistics and Crash Reports
- Reset All Warning Messages
- Set the Default Location for Opening and Saving Files
- Set the Default Author For Files and Collections
- Set the Ancestor Limit for History Trees
- Set the Default Export Formats
- Set the Default Export Formats (SnapGene 6.0 or earlier)
- GenBank Export Customization
- Set the "Molecule Type" for Imported GenBank Files
- Prohibit /label Qualifiers in Exported GenBank Files
- Transfer Source Features During Cloning Simulations
- Set the Default Display Preferences for New Collections
- Set the Display Preferences for New and Imported DNA Sequences
- Set the Display Preferences for New and Imported RNA Sequences
- Display Feature Labels Below or Inside a Map
- Italicize Restriction Enzyme Names
- Don't Highlight Unique Cutters in Bold
- Highlight Blunt Cutters in Green
- Set the Default Primer Hybridization Parameters Used for New or Imported Sequences
- Show Full Structures for Primer-Template Duplexes
- Set the Default Display Preferences for New Protein Sequences
- Prohibit Region Labels Above a Protein Map
- Show Protein Molecular Weights in Daltons
- Set the Default Stringency for Hiding Chromatogram Ends
- Set Preferences for Agarose Gel Simulations
Display Options for DNA Sequences
- Change View Options for DNA Sequences
- Display a Circular Plasmid as a Linear (Horizontal) Map
- Show or Hide DNA Feature Labels
- Show Restriction Site or Primer Coordinates on a Map
- Show Features on the DNA Line
- Display a DNA Sequence Minimap
- Display Sequence as Plain Text
- Show a Translated CDS in 3-Letter Format
- Display the reverse complement of a dsDNA sequence
- Move the origin in a plasmid
- Set the Origin Coordinate for a Linear Sequence
- Adjust Line Width in Sequence View
- Show or Hide Sequences Aligned to a Reference Sequence
- View Sequence in Blocks of 3 or 10
Display Options for Protein Sequences
- Change View Options for Protein Sequences
- Show or Hide Protein Features
- Customize Protein Sequence Colors
- Show or Hide Protein Colors
- Hide or Show Protein Region Labels
- Show or Hide Protein Feature Numbering in Map View
- Show or Hide a Protein Minimap in Sequence View
- Show a Protein Sequence in Compact Format
- Display a Protein Sequence with One or Three Letter Amino Acid Codes
- Change the Protein Sequence Line Width
Other Display Options
- Show or Hide the Toolbars
- Change the Font Size
- View a Sequence with a Split Window
- View Sequence Traces with Color Vision Disabilities
- Show a Plot of GC Content
- View an AB1 or SCF Trace File
- Show DNA/RNA Calculations
Description Panel
- Show or Hide the Description Panel
- Add Descriptive Information to a Sequence File
- Add Reference Information to a Sequence File
- Embed Files from Other Programs in a Sequence File
Enzymes
- Show or Hide Individual Enzymes
- Choose an Enzyme Set
- Choose Enzymes Manually
- Highlight an Enzyme Site
- Display a Restriction Site Overview
- Sort Enzymes
- View Enzyme Information
- View Noncutters
- Save or Export Enzyme Set
- Manage Enzyme Sets
- Set the Preferences for Enzymes
- Add a Restriction Site to a Coding Sequence Without Changing the Translation
- Remove a Restriction Site From a Coding Sequence Without Changing the Translation
Features
- Create a Simple Feature
- Create a Translated Feature
- Adjust Translated Feature Numbering
- Create a Feature Segment
- Annotate Introns
- Add a Cleavage Arrow
- Create a Point Feature
- Edit Multiple Features
- Delete Features
- Confirm an In-Frame Gene Fusion
- Set the Genetic Code for a Feature
- Designate a Non-ATG Start Codon
- Show or Hide Features
- Sort the Feature List
- Import Feature Data
- Export Feature Data
- Splice to Remove Introns
- Detect Common Features
- Detect Custom Features
- Edit Common Features
- Share Custom Feature List
- Add Reference Information to a Feature
- Create a Feature with Introns Using an Aligned cDNA
- Prioritize Display of Features in Map View
- Edit Feature Qualifiers
Custom Feature Types (SnapGene 6.0 and later)
- Standard Feature Types in SnapGene
- Create Custom Feature Types
- Manage Custom Feature Types
- Add a Custom Feature Type to a Sequence
- Import Custom Feature Types in a File
- Share Custom Feature Types via a Delimited List File
Primers
- Create a Primer
- Edit Multiple Primers
- Adjust Primer Hybridization Parameters
- Show or Hide Primers
- Sort the Primers List
- Import Primers
- Export Primers
- Analyze Primer Sequences
Translations
- Show or Hide Translations and ORFs
- Choose the Translation Frames
- Choose the Translation Format
- Choose the Translation Genetic Code
- Display Open Reading Frames
- Convert an ORF to a Feature
Colors
- Customize DNA Sequence Colors
- Show or Hide DNA Colors
- Choose a Color Mode
- Show Colors in History View
Searching
- Search for an Exact DNA Sequence
- Search for Similar DNA Sequences
- Search for a Protein Sequence
- Search for an Enzyme, Feature, or Primer
Zooming
- Show or Hide the SnapGene Zoom Controls
- Zoom In
- Pan Across a Sequence
History
- What is SnapGene History View?
- View, Print or Copy History as Text
- Trim History
RNA
- Create an RNA File
- Import an RNA File
- Align RNA Files
- Convert RNA to DNA
- View Predicted RNA Secondary Structure
Proteins
- Create a Protein Sequence
- Import a Protein Sequence
- Make a Protein Sequence from a DNA Sequence
- Show Protein Properties
Restriction Cloning and Linear Ligation
- Insert a Fragment into a Plasmid
- Insert Multiple Restriction Fragments into a Plasmid
- Delete Restriction Fragment
- Destroy a Restriction Site
- Linear Ligation
- Golden Gate Assembly
- Concatenate Sequences
Gateway Cloning®
- Simulate Gateway® Cloning with One Insert
- Simulate Gateway® Cloning with Multiple Inserts
Gibson Assembly®
- Simulate Gibson Assembly® with One Insert
- Simulate Gibson Assembly® with Multiple Inserts
- Circularize a Fragment by Gibson Assembly®
NEBuilder HiFi DNA Assembly®
- Simulate NEBuilder HiFi DNA Assembly® with One Insert
- Simulate NEBuilder® Hifi DNA Assembly with Multiple Inserts
- Circularize a Fragment by NEBBuilder® HiFi DNA Assembly
In-Fusion® Cloning
- Simulate In-Fusion® Cloning with One Insert
- Simulate In-Fusion® Cloning with Multiple Inserts
TA or GC Cloning
- Simulate TA or GC Cloning
TOPO® Cloning
- Simulate Directional TOPO® Cloning
- Simulate TA TOPO® cloning
- Simulate Blunt TOPO® Cloning
Golden Gate Assembly
- Golden Gate Cloning of a Single Fragment into a Vector
- Golden Gate Cloning of Multiple Fragments into a Vector with Type IIS Sites
- Golden Gate Cloning of Multiple Fragments into a Vector with no Golden Gate sites
- Golden Gate Cloning into a Vector Cut with non-Type IIS Enzymes
- Set the Enzymes for Golden Gate Assembly
- How is Golden Gate Fidelity Predicted in SnapGene?
PCR and Mutagenesis
- PCR
- Inverse PCR
- Overlap Extension PCR
- Mutagenesis
Agarose Gel Simulation
- Create an Agarose Gel
- Save an Agarose Gel
- Choose a MW Marker
- Set the Default MW marker
- Configure the Gel Properties
- Choose a Sequence for Digestion or PCR
- Simulate a Restriction Digest
- Simulate a PCR Amplification
- Rearrange the Gel Lanes
- Export the Gel Data
- Customise the MW marker List
Collections
- Make a New Collection
- Collection Areas
- Designate a Main Collection
- Open a Collection
- Add Files to a Collection
- Organize Sequences in a Collection
- Import from a Database to a Collection
- Export Files from a Collection
- Save Changes in a Collection
- Adjust the Collection Display Options
- Permanently Change a Collection's Display Settings
- Rename a File or Folder in a Collection
- Search a Collection
- Do Bulk Replacement in a Collection
- Define a Working Set in a Collection
- Specify a Description and Authors for a Collection
- Configure Code Numbers for a Collection
- Create Links Between Collection Areas
- Bulk edit the Description Information of multiple Sequences
Batch Operations
- Add Description Data to Multiple Sequences
- Add Common Features to Multiple DNA Sequences
- Import Features into Multiple SnapGene Files
- Import Primers into Multiple SnapGene Files
- Flip Multiple DNA Sequences
- Blast Multiple Sequences
- Batch Convert Sequence Files to a New Format
- Batch Trim File Histories
Importing and Exporting
- Import a Sequence from NCBI
- Import a Multisequence FASTA or GenBank File
- Import a Published Plasmid Sequence
- Import a Vector NTI Database
- Import Features from a GTF, GFF3, or BED File
- Import a BAM or SAM File
- Export a DNA Sequence
- Export Part of a DNA Sequence
- Export an Alignment
- Export a Protein Sequence
- Export Part of a Protein Sequence
- Export a DNA, RNA or Protein Map as an Image
- Export the Consensus from a DNA or Protein Multiple Alignment
Editing Sequences
- Create a New DNA or RNA Sequence
- Edit a DNA or RNA sequence
- Edit a Sanger (.ab1, .scf or .ztr) Trace File
- Edit DNA Ends
- Circularize or Linearize a DNA Sequence
- Extract a Restriction Fragment from a Sequence
- Extract a Region in a Sequence to a New File
- Edit the Sequence Name Label
- View or Use IUPAC Ambiguity Codes
- Copy a DNA or RNA Sequence to the Clipboard
Assembly and Alignment
- De Novo Assembly of Sanger Sequences
- Align Sanger Reads to a Reference Sequence
- Force a Read to Align to a Specific Repeat Region
- Force a Read to Align to a Specific Inverted Repeat Region
Pairwise and Multiple Alignment
- Create a Pairwise DNA Alignment
- Create a Pairwise Protein Alignment
- Create a Multiple Sequence Alignment
- Reorder or Rename Sequences in a Multiple Alignment
- Repeat an Alignment with an Alternative Algorithm, New Parameters or Changed Input
- Convert a DNA Alignment to a Protein Alignment
- View Features in Multiple Sequence Alignments
- View or Edit Features in a Multiple Alignment
- View or Edit Features in a Pairwise Alignment
Single Stranded Sequences
- Create or Import a Single-Stranded DNA Sequence
- Convert Between Single-Stranded and Double-Stranded Formats
Designing Sequences
- Design a Synthetic Construct
- Insert a Restriction Enzyme Site into a Sequence
- Insert Codons into a Sequence
- Insert a Feature into a Sequence
- Order a Synthetic Sequence
- Insert a Back-Translated Protein into a DNA Sequence
- Anneal Oligonucleotide Pairs
Codon Usage
- Show Codon Frequencies
- Reverse Translate a Protein
- Import or Create a Codon Usage Table
- Change Codons in a Coding Sequence (CDS) Based on a Codon Usage Table
Electronic Laboratory Notebooks
- Exchange Files with the LabArchives ELN
Command Line Interface
- Command Line: Converting File Formats
- Command Line: Creating Maps of DNA Sequences
Blast
- Blast a Sequence
- Blast Multiple Sequences
Localization
- Set the Language for SnapGene
ShortCuts
- Keyboard and Gesture Shortcuts