Home Page
User Guide to SeqBuilder Pro — 17.4
  • 17.5
  • 17.4
Table of Contents
Home Page
  • User Guide to SeqBuilder Pro — 17.4
    • User Guide to SeqBuilder Pro — 17.5
    • User Guide to SeqBuilder Pro — 17.4
  • 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
    • 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
  • Select an Object or Range
  • 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
      • Feature Library Manager
    • Specify the features to use 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

Step 1: Start a cloning project and specify the insert

The first step in performing a cloning simulation is to specify the insert. The following topics describe six different methods of specifying the insert to use with your cloning project:

  • 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
Create a custom vector for directional TOPO cloning
Option A – Use a sequence file on your computer as the insert

Need more help with this?
Contact DNASTAR

Thanks for your feedback.
Copyright DNASTAR, Inc. 2022