Try it! – Gateway cloning

Automated Virtual Cloning » Try it! – Gateway cloning

Gateway cloning is based upon the site-specific recombination of lambda bacteriophage, and is a two-part process. In the first part of the tutorial, you will create a Gateway entry clone. In the second part, you will use the entry clone as input for constructing the…

Try it! – MultiSite Gateway Pro cloning

Automated Virtual Cloning » Try it! – MultiSite Gateway Pro cloning

MultiSite Gateway Pro technology enhances the classic Gateway cloning protocol by allowing you to clone up to four regions at one time. In MultiSite Gateway Pro cloning, three additional types of recombination sites have been engineered to recombine uniquely between…

Try it! – Create and modify a feature

Sequence Editing and Annotation » Features » Try it! – Create and modify a feature

In the following tutorial, you’ll locate open reading frames (ORFs), create a feature at the location of a pair of ORFs, and then change the way the feature is displayed. If you have not yet download and extracted the tutorial data, click here to download it.…

Try it! – Use a PCR insert in restriction cloning

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option E – Use the PCR product of the current primer pair as the insert » Try it! – Use a PCR insert in restriction cloning

The tutorial Try it! – Create and edit primers for use in restriction cloning showed how to add restriction enzymes to a sequence. This tutorial demonstrates how to cut and clone the histidine kinase gene into the desired vector. Follow the steps in Try it!…

Try it! – Create and modify primers for TA cloning

Primers » Edit primers » Introduce a codon change or mutation » Try it! – Create and modify primers for TA cloning

To create a primer pair for a region of interest on the sequence to use in TA cloning: If you have not yet download and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. Use File >…

Try it! – Apply a restriction enzyme to the sequence

Enzymes » Show or hide enzymes in other views » Try it! – Apply a restriction enzyme to the sequence

In this short tutorial, you’ll remove the restriction enzymes displayed on the sequence by default, and instead display only the DraI enzyme cut sites: If you have not already done so, follow the tutorial Try it! – Create and modify primers for TA…

Try it! – Open an Entrez sequence by accession number

Sequence Editing and Annotation » Sequence editing » Open an existing sequence » Open a sequence from an online database » Open an Entrez database file by locus name or accession number » Try it! – Open an Entrez sequence by accession number

In this part of the tutorial, you will open a histone DNA sequence from NCBI’s Entrez database. In order to complete this tutorial, your computer must be connected to the Internet. Select File > Open Entrez Sequence. The Open Entrez dialog appears. Under…

Try it! – Use a PCR insert in TA cloning

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option E – Use the PCR product of the current primer pair as the insert » Try it! – Use a PCR insert in TA cloning

The tutorial Try it! – Create and modify primers for TA cloning demonstrated how to select and modify a primer pair. This tutorial shows how to extract the PCR insert and create a virtual TA clone. If you have not already done so, follow the tutorial Try it!…

Try it! – Create and modify primers for restriction cloning

Primers » Edit primers » Introduce restriction sites » Try it! – Create and modify primers for restriction cloning

In this tutorial, you will prepare for restriction cloning by creating primer pairs for a gene of interest, and then manually introducing restriction sites. If you have not yet download and extracted the tutorial data, click here to download it. Then decompress…

Try it! – Gibson cloning with a custom vector

Automated Virtual Cloning » Try it! – Gibson cloning with a custom vector

The Vectors drop-down menu in the Project window is a shortcut to all of the vectors contained in the CloningVectors.sbp project, also known as the “Vector Catalog.” It is possible to add a custom vector to an open project, or to add it to the Vector Catalog…

Try it! – Create a style set for CDS features

Plasmid 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

The Feature Library Manager can be used to specify how to display particular features or groups of features when auto-annotating plasmids/vectors in the Annotation Results window. This tutorial shows how to specify a particular style for displaying all CDS…

Try it! – Find restriction sites on either side of a feature

Enzymes » Create and manage sets of enzymes » Try it! – Find restriction sites on either side of a feature

In this tutorial, you will look for a single enzyme capable of excising a histone coding feature from a sequence named X05543.1. To open the sequence, follow the tutorial Try it! – Open an Entrez sequence by accession number. You’ll need an enzyme that…

Download and extract tutorial data

Appendix » Download and extract tutorial data

Before beginning a tutorial (“Try it!” topic), you may need to download data from the DNASTAR website: Go to the DNASTAR Training page. Click on SeqBuilder Pro to expand its section. To the right of Written Tutorial Data, click the name of your…

Sequence Editing and Annotation

Sequence Editing and Annotation

      Did you arrive here by selecting the   DNASTAR Navigator workflow Molecular Biology > Sequence editing and annotation? If so, you’re in the right place!       SeqBuilder Pro lets you single or…

Step 5: Run the cloning simulation

Automated Virtual Cloning » Step 5: Run the cloning simulation

When you have specified the insert and vector, and set up additional options as desired, you are ready to begin the cloning simulation: Press the Try It or Clone button in the bottom right corner of the Project window. The view switches from the Clone tab to the…

Specify the appearance of features in the Feature Library Manager and Annotation Results window

Plasmid Auto-Annotation » Specify the appearance of features in the Feature Library Manager and Annotation Results window

You can use the tools at the top of the Feature Library Manager to control how features are displayed in the Manager, itself, and in the Annotation Results window after performing the auto-annotation procedure. This step is entirely optional. For example, you could…