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User Guide to SeqBuilder Pro — 17.3
18.0
Table of Contents
Home Page
User Guide to SeqBuilder Pro — 17.3
User Guide to SeqBuilder Pro — 18.0
Welcome to SeqBuilder Pro
SeqBuilder Pro Tutorials
Open an Existing Sequence
Open a local sequence
Change the default application for opening Lasergene files
Open a sequence from the Project window
Open a sequence from an online database
Specify URLS for BLAST and Entrez Searches
Open an Entrez database file by locus name or accession number
Try it! – Open an Entrez sequence by accession number
Open an Entrez database file using a text search
Entrez Search Results window
View search results in a web browser
Open results in a Lasergene application
Print search results
Copy search results
Save search results
Specify a download folder for online search results
Open a BLAST database file using a similarity search
BLAST Search Results window
Import a Vector NTI database
Create a New Sequence
IUPAC codes
Use editing commands
Select an Object or Range
Go to a location on a sequence
Create Sequences Based on Other Sequences (Batch Editing)
Create reverse complements of multiple sequences
Create translations of multiple sequences
Create one sequence from multiple sequences
Create sequences from features in another sequence
Export sequences into a single file
Create a file by sampling sequences
Windows, Views, Panels and Tools
Document window views
Circular view
Linear view
Sequence view
Primer Design view
Primer Design tools
Quality score calculation
Features view
Primers view
Comment view
Minimap view
Site Summary view
History view
Gel Simulation view
Fragment Sizes view
Document window panels
Style panel
Enzymes panel
Enzymes panel for gels
Enzymes panel for other situations
Settings panel
Settings panel for gels
Settings panel for other situations
Details panel
Sequences panel
Primers panel
Markers panel
Shared button tools
Project window
Find a sequence in the Project window
Customize the Sequence Display
Change the rendering style or font
Move an object or row
Use preset layouts or create new ones
Handle overlapping graphics
Zoom in or out
Enzymes
Create and manage individual enzymes
Enzymes with unusual cleavage properties (Bgh I and Taq II)
Create and manage sets of enzymes
Enzyme Selector Manager
Try it! – Find restriction sites on either side of a feature
Apply or remove enzymes in the Gel Simulation view
Show or hide enzymes in other views
Try it! – Apply a restriction enzyme to the sequence
Example of showing potential cuts at ambiguous bases
Change the way enzymes are displayed
View cut sites and recognition sequence
ORFs
Translations
Choose the genetic code
Modify the genetic code
Rulers
Features
Create or delete features
Edit information about a feature
Try it! – Create and modify a feature
Show or hide features
Join feature segments
Primers
Create primer pairs automatically
Create a primer based on a selected region of sequence
Import primers
Pair primers manually
Edit primers
Change the name of a primer
Modify a base in the primer
Modify the primer length
Introduce a codon change or mutation
Try it! – Create and modify primers for TA cloning
Introduce restriction sites
Choose, show or hide primers
Export primers
Delete primers
Methods used in primer design
Thermodynamic models
Pentamer profile
Annealing temperature
Melting temperature
Plasmid Auto-Annotation
Create a custom feature database for auto-annotation searches
The Feature Library Manager
Specify the features to use or exclude in auto-annotation
Specify the appearance of features in the Feature Library Manager and Annotation Results window
Try it! – Create a style set for CDS features
Perform the auto-annotation procedure
Annotation Results Window
Automated Virtual Cloning
Preliminary Step (optional): Add custom vectors to the cloning vector catalog
Create a custom vector for Gateway cloning
Create a custom vector for TA cloning
Create a custom vector for directional TOPO cloning
Step 1: Start a cloning project and specify the insert
Option A – Use a sequence file on your computer as the insert
Option B – Copy inserts from another SeqBuilder Pro cloning project
Option C – Use an entire open SeqBuilder Pro sequence as the insert
Option D – Use part of an open SeqBuilder Pro sequence file as the insert
Option E – Use the PCR product of the current primer pair as the insert
Option F – Use restriction enzyme cut sites to create the insert
Step 2: Specify the method and options
Available cloning methods
Step 3: Specify the vector and entry clone
Step 4: Digest/linearize a circular vector
Step 5: Run the cloning simulation
Step 6 (optional): Verify the clone
Interpret results from clone verification
Step 7: View and print cloning results
Try it! – Gateway cloning
Try it! – MultiSite Gateway Pro cloning
Try it! – Gibson cloning with a custom vector
Try it! – PCR-directed restriction cloning
Try it! – Use a PCR insert in TA cloning
Automated Batch Cloning
Site-Directed Mutagenesis
Agarose Gel Simulation
Sequence Statistics
Motion Library
Copy, Print, Save and Export
Copy a sequence or image
Print on Windows
Print on Macintosh
Save
Export sequences
Close and Exit
Appendix
Research references
Installed Lasergene file locations
Installed enzyme file locations
Turn off usage logging
Download as PDF
Appendix
Close and Exit
Research references
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