Search - User Guide to SeqBuilder Pro

Export sequences into a single file

Create Sequences Based on Other Sequences (Batch Editing) » Export sequences into a single file

To create a single multi-sequence file composed of exported sequences: Choose Tools > Export Sequences into Single File. The Project window opens with the Project and Options tabs active. In the Project tab, place the sequences you wish to export into the…

Export sequences

Copy, Print, Save and Export » Export sequences

To export one or more sequences in the Project window to individual sequence files: To do this, you must have already imported one or more sequences to the Project window. Select one or more sequences from the Project tab. Choose File > Export Sequence(s) From…

Create a file by sampling sequences

Create Sequences Based on Other Sequences (Batch Editing) » Create a file by sampling sequences

The Tools > Sample By command is used to create an output file that contains a filtered set of sequences from a source file. Source file sequences can be filtered according to one or more specified conditions, such as length, contents, and start/end sequence…

Sequences panel

Windows, Views, Panels and Tools » Document window panels » Sequences panel

The Sequences panel, represented by a circular sequence icon, lets you choose which sequence to use when performing an agarose gel simulation. This panel is enabled only after you use the File > New Agarose Gel command. Sequences that were open in the Document window…

Create Sequences Based on Other Sequences (Batch Editing)

To create new sequences related to locally-stored sequences SeqBuilder Pro 15.1 and later support batch sequence editing. See the following topics to learn how to create new sequences: …by reverse complementing one or more sequences …by translating…

Export primers

Primers » Export primers

To export primers: Create or import primers. Open the Primers view. Choose File > Save Primer Catalog. Select one of the following three formats: Tab-delimited text (.txt) – Values from the Set Name, Pair Name, T/B, and Primer Sequence…

Create translations of multiple sequences

Create Sequences Based on Other Sequences (Batch Editing) » Create translations of multiple sequences

To translate one or more nucleic acid sequences into protein sequences using a specified translation table: Choose Tools > Batch Translate. The Project window opens with the Project and Options tabs active. In the Project tab, the sequences you wish to…

Open a BLAST database file using a similarity search

Open an Existing Sequence » Open a sequence from an online database » Open a BLAST database file using a similarity search

To perform a BLAST search: Select the sequence or portion of sequence that you want to search for. Choose Net Search > BLAST Selection. The Server field lists the currently selected BLAST server. You may change to a different server by choosing one…

Go to a location on a sequence

Create a New Sequence » Go to a location on a sequence

To go to a numerical position or select a range on the sequence: Choose Edit > Go To Position or use the keyboard shortcut Ctrl/Cmd+J. Type the desired position or range into the box in the dialog. To specify a range, type in the left coordinate, then two…

Create reverse complements of multiple sequences

Create Sequences Based on Other Sequences (Batch Editing) » Create reverse complements of multiple sequences

To reverse complement one or more sequences: Choose Tools > Batch Reverse Complement. The Project window opens with the Project and Options tabs active. In the Project tab, the sequences you wish to reverse complement should be placed in the Sequences…

Create one sequence from multiple sequences

Create Sequences Based on Other Sequences (Batch Editing) » Create one sequence from multiple sequences

To join two or more sequences end-to-end: Choose Tools > Concatenate. The Project window opens with the Project and Options tabs active. In the Project tab place the sequences you wish to join into the Sequences folder. To add sequences to a folder, select…

Create sequences from features in another sequence

Create Sequences Based on Other Sequences (Batch Editing) » Create sequences from features in another sequence

To create new sequences from existing sequence features: Choose Tools > Extract Features as Sequences. The Project window opens with the Project and Options tabs active. In the Project tab, place the sequences whose features you wish to extract into the…

Option A – Use a sequence file on your computer as the insert

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option A – Use a sequence file on your computer as the insert

From the Cloning menu, select one of the following commands: Gibson, LIC Cloning; In-Fusion Cloning, GeneArt Cloning; MultiSite Gateway Pro Cloning; Gateway Expression Clone; Gateway Entry Clone; Restriction Enzyme Cloning; TA Cloning; Directional TOPO Cloning. …

Open an Entrez database file using a text search

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search

SeqBuilder Pro provides a graphical interface for constructing Boolean queries of text databases like NCBI’s Entrez database. Search results are returned as a list from which you may select any or all sequences, then save them or open them as documents in the current…

Copy, Print, Save and Export

From within SeqBuilder Pro, you can do the following: Copy a sequence or image Print (Windows / Macintosh) Save Export sequences

Installed enzyme file locations

Appendix » Installed enzyme file locations

SeqBuilder Pro contains representatives of a wide variety of restriction sites for available enzyme isotypes. By default, Lasergene’s enzyme and enzyme selector files are installed in the following directory: Windows: C:\Program Files (x86)\DNASTAR\Lasergene…

Installed Lasergene file locations

Appendix » Installed Lasergene file locations

The following file names use ‘x’ to represent the version number. File Category Application Path Application2 ArrayStar Windows: C:\Program Files (x86)\DNASTAR\Lasergene x\ArrayStar SeqNinja (command line) Windows:…

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…

Welcome to SeqBuilder Pro

SeqBuilder Pro is Lasergene’s application for sequence editing and map creation, as well as plasmid auto-annotation, automated virtual cloning and primer design. Easily navigate between synchronized views with a click of a button, and rearrange views and toolbars…

Open a local sequence

Open an Existing Sequence » Open a local sequence

To open a local sequence file: Choose File > Open or use the keyboard shortcut Ctrl/Cmd+O to open a nucleotide or protein sequence. If the sequence shape (circular or linear) is not defined in the file, SeqBuilder Pro will assume the sequence is linear. When using…

Create a New Sequence

The following video is a brief overview of sequence creation and editing in SeqBuilder Pro. To create a new DNA or protein sequence from scratch: Choose the appropriate menu command or keyboard shortcut. DNA: File > New DNA or Ctrl/Cmd+N. Protein:…

Create a primer based on a selected region of sequence

Primers » Create a primer based on a selected region of sequence

To create a primer based on a selected region of sequence: Open the Primer Design view. Select some or all of the sequence. Select Priming > Create Forward Primer to create the primer on the forward strand, or Priming > Create Reverse Primer to create the…

Edit information about a feature

Features » Edit information about a feature

To edit information about a feature: Open the Features view. Expand the row(s) for the feature(s) of interest: Expand a single row by clicking on the plus sign on the left of the row. Expand all rows by right-clicking anywhere in the view and…

Copy a sequence or image

Copy, Print, Save and Export » Copy a sequence or image

To copy selected text (including sequence) to the clipboard: Choose Edit > Copy or use the keyboard shortcut Ctrl/Cmd+C. To copy selected text that will be pasted in a particular format: Use Edit > Copy As. Unformatted Sequence – Copies the sequence…

Import a Vector NTI database

Open an Existing Sequence » Open a sequence from an online database » Import a Vector NTI database

Invitrogen’s Vector NTI software will no longer be sold after December 31, 2019. In preparation for this event, Vector NTI users are encouraged to move their databases to SeqBuilder Pro using the following automated method: Download the Vector NTI Data Export…

Open an Entrez database file by locus name or accession number

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file by locus name or accession number

If you know the locus name or accession number for a sequence, SeqBuilder Pro can retrieve it from the Entrez database at the National Center for Biotechnology Information (NCBI): Use File > Open Entrez Sequence or the keyboard shortcut Ctrl/Cmd+R. The Server…

Modify a base in the primer

Primers » Edit primers » Modify a base in the primer

To modify a base in the primer: Create or import primers or primer pairs. Modify bases using either of these methods: For single primers only (i.e., the primer cannot be part of a primer pair) – From within the Primers view, click inside the Primer…

Introduce a codon change or mutation

Primers » Edit primers » Introduce a codon change or mutation

To introduce a codon change or mutation: Create or import primers or primer pairs. Open the Primer Design view. Select the Introduce Codon Change/Mutation tool ( ) at the top left of the window; or choose Priming > Introduce Codon Change/Mutation. Click…

Open results in a Lasergene application

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window » Open results in a Lasergene application

To open one or more results from the Entrez or BLAST Search Results windows: Select one or more results from the Search Results window using click, Ctrl/Cmd+click, or Shift+click, or by adding a checkbox to the left of the row(s) of interest. Do any of the…

Change the name of a primer

Primers » Edit primers » Change the name of a primer

Once you have created primers, you can change the name of the primer as follows. Open the Primer Design view. Expand the primer row by clicking on the plus sign. In the Name column, click on the cell for the name you wish to change. Type a new name into…

Find a sequence in the Project window

Windows, Views, Panels and Tools » Project window » Find a sequence in the Project window

To find a sequence in the Project window : Select Edit > Find. Specify the search criteria as follows: Search sequence names for: To search for sequences whose names contain the text input in this text box. Search bases for: To search for sequences…

Open a sequence from the Project window

Open an Existing Sequence » Open a sequence from the Project window

To open one or more sequences from the Project window : Open a populated Project window by selecting it from the Window menu. Select the desired sequences using click, Shift+click or Ctrl/Cmd+click. Choose File > Open Selections. If you have selected…

Open a sequence from an online database

Open an Existing Sequence » Open a sequence from an online database

SeqBuilder Pro’s Net Search menu allows you to search online databases (e.g., the National Center for Biotechnology Information’s BLAST and Entrez servers), for sequences that match all or part of the current sequence. Once a match has been located, you may add it…

View search results in a web browser

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window » View search results in a web browser

To view one or more results from the Entrez or BLAST Search Results windows in a web browser: Do either of the following: Double-click on any result from the window. Select one or more results from the window using click, Ctrl/Cmd+click, or Shift+click, or by…

Step 4: Digest/linearize a circular vector

Automated Virtual Cloning » Step 4: Digest/linearize a circular vector

After you specify the vector or entry clone, a Digest or Linearize button may appear. This button lets you specify where in the vector to insert the fragment. The appearance (or not) and name of this button depends on which method you chose, and whether your vector is…

Create a custom vector for Gateway cloning

Automated Virtual Cloning » Preliminary Step (optional): Add custom vectors to the cloning vector catalog » Create a custom vector for Gateway cloning

If desired, a Gateway cloning vector may be constructed manually and then added to the Cloning Vector Catalog prior to beginning the cloning workflow. Prepare the vector as follows and refer to the example at the bottom of this topic. Set the type to circular by…

Create a custom vector for TA cloning

Automated Virtual Cloning » Preliminary Step (optional): Add custom vectors to the cloning vector catalog » Create a custom vector for TA cloning

If desired, a T-vector for TA cloning may be constructed manually and then added to the Cloning Vector Catalog prior to beginning the cloning workflow. To make the vector recognizable for TA cloning, a specific overhang must be created on both strands at the 3’…

Option D – Use part of an open SeqBuilder Pro sequence file as the insert

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option D – Use part of an open SeqBuilder Pro sequence file as the insert

Use File > Open to open the file or SeqBuilder Project (.sbd) containing the sequence fragment you wish to clone. Use any of the following methods to select the sequence fragment to use as the insert: Manually select a portion of sequence by dragging the…

Specify the features to use in auto-annotation

Plasmid Auto-Annotation » Specify the features to use in auto-annotation

To specify the features to use in auto-annotation: Specifying which features to use in auto-annotation is optional. Choose Features > Feature Library Manager. This automatically loads the installed database file named feature.library. The Feature list on the left…

Try it! – Create and modify a feature

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.…

Specify a download folder for online search results

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window » Save search results » Specify a download folder for online search results

To specify a download folder for results from an Entrez or BLAST Search Result window: Depending on your Lasergene version, choose Edit > Preferences or Settings (Windows) or SeqBuilder Pro > Preferences or Settings (Mac). Select the Internet tab. (optional)…

Create a custom vector for directional TOPO cloning

Automated Virtual Cloning » Preliminary Step (optional): Add custom vectors to the cloning vector catalog » Create a custom vector for directional TOPO cloning

If desired, a directional TOPO cloning vector may be constructed manually and then added to the Cloning Vector Catalog prior to beginning the cloning workflow. To make the vector recognizable for directional TOPO cloning, a specific overhang must be created at the…

Create a custom feature database for auto-annotation searches

Plasmid Auto-Annotation » Create a custom feature database for auto-annotation searches

When you auto-annotate vector sequences, SeqBuilder Pro searches for potential matches in the installed Feature Library, and in a custom database of features named “User” features. Creating a custom “User” database is optional. To create a “User”…

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…

Step 1: Start a cloning project and specify the insert

Automated Virtual Cloning » 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…

Try it! – Use a PCR insert in TA cloning

Automated Virtual Cloning » 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!…

Option F – Use restriction enzyme cut sites to create the insert

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option F – Use restriction enzyme cut sites to create the insert

Use File > Open to open the file or SeqBuilder Pro project (.sbd) containing the vector sequence. Use the Enzymes tool ( ) to apply the set of Unique Sites. When you find suitable left and right cut sites, select the region between them by clicking on the…

Preliminary Step (optional): Add custom vectors to the cloning vector catalog

Automated Virtual Cloning » Preliminary Step (optional): Add custom vectors to the cloning vector catalog

A comprehensive cloning vector catalog named CloningVectors.sbp is installed with Lasergene. Before you begin a cloning project, you can create and add custom vectors to this catalog to use with current and future projects. As you update Lasergene in the future,…

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…

Project window

Windows, Views, Panels and Tools » Project window

The Project window is a single- or multi-tabbed window that launches in the following situations: Choosing File > New Project The window opens with an unpopulated folder named New Folder in the Project tab. Choosing File > New Cloning Project The window opens…

Save

Copy, Print, Save and Export » Save

You can save a sequence or project using File > Save (Project) or File > Save As (Project). See the table below for restrictions. Most SeqBuilder Pro projects are saved with the extension .sbd (single document project) or .sbp (multiple document project), but agarose…

Save search results

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window » Save search results

To save selected results from the Entrez or BLAST Search Results windows as a text file: (optional) Specify a default download folder for online search results. Make the Entrez or BLAST Search Results window the active window. Select File > Save As. By…

Apply or remove enzymes in the Gel Simulation view

Enzymes » Apply or remove enzymes in the Gel Simulation view

After using File > New Agarose Gel to initiate an agarose gel simulation, a specialized version of the Enzymes panel can be used to apply or remove enzymes from a lane in the Gel Simulation view. To apply enzymes to an agarose gel lane: First select a non-empty gel…

Agarose Gel Simulation

Agarose gel simulation lets you find the location of restriction enzymes on a gel and perform ‘mock’ digests to determine the expected size of digest products on an electrophoresis gel. Gel simulations let you find the ideal percent agarose and set of molecular…

Create primer pairs automatically

Primers » Create primer pairs automatically

To design primer pairs: Open the Sequence, Linear, Circular or Minimap view and use the mouse to select the region you wish to amplify. If none of the sequence is selected, the entire sequence will be amplified. Choose Priming > Create Primer Pairs. In the Create…

Print search results

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window » Print search results

To print results from the Entrez Search Results window: Select one or more results from the Search Results window using click, Ctrl/Cmd+click, or Shift+click, or by adding a checkbox to the left of the row(s) of interest. Click the Print button to proceed with…

Plasmid Auto-Annotation

SeqBuilder Pro’s built-in plasmid Feature Library contains over 150 curated features, and allows you to add your own features, as well. If your vector sequences lack some annotations, or contain incomplete or obsolete versions of annotations, you can…

Translations

SeqBuilder Pro lets you view the translation for part or all of an open nucleotide sequence or create a new protein sequence based on the translation of a nucleotide sequence. To display translations for an open nucleotide sequence: In the Sequence or Primer Design…

Sequence Statistics

To view a statistical summary of a selected portion of sequence: Select a portion of the sequence in a graphical view. Choose Sequence > Statistics. For nucleotide sequences, the display shows the number and composition of bases, the percentage of A, G,…

Thermodynamic models

Primers » Methods used in primer design » Thermodynamic models

The stability of a particular double stranded sequence is related to the number of hydrogen bonds formed. GC rich sequences pair with greater stability than AT rich sequences, but sequence ordering is also a component of stability. For example, the duplex AA/TT forms a…

Automated Batch Cloning

Automated batch cloning lets you automatically clone large numbers of fragments into the same vector. Most of the steps involved are similar or identical to those in regular automated virtual cloning, but the cloning window has been optimized for batch…

Sequence view

Windows, Views, Panels and Tools » Document window views » Sequence view

The Sequence view is one of the ten is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Sequence tab ( ). The Sequence view…

Perform the auto-annotation procedure

Plasmid Auto-Annotation » Perform the auto-annotation procedure

If your vector sequences lack some annotations, or contain incomplete or obsolete versions of annotations, the following procedure lets you effortlessly copy features from a curated Feature Library, or from your own custom features, to the query sequences. Conversely,…

Automated Virtual Cloning

SeqBuilder Pro supports automated virtual cloning using a wide variety of cloning techniques. Simply select your insert and vector sequences, and SeqBuilder Pro will automatically construct the virtual clone. Choose vectors from the vector catalog provided, or add your…

Entrez Search Results window

Open an Existing Sequence » Open a sequence from an online database » Open an Entrez database file using a text search » Entrez Search Results window

When an Entrez database search is complete, the Entrez Search Results window appears, showing a list of sequences that match your query. The buttons at the top of the window are used to open, save, copy or print results. Task Button to…

Enzymes with unusual cleavage properties (Bgh I and Taq II)

Enzymes » Create and manage individual enzymes » Enzymes with unusual cleavage properties (Bgh I and Taq II)

Most restriction enzymes follow a simple cutting pattern, with one forward and one reverse cut site. Several enzymes have two forward and two reverse cut sites. For these enzymes, two restriction sites need to be entered into the database rather than one. For example,…

Comment view

Windows, Views, Panels and Tools » Document window views » Comment view

The Comment view is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Comment tab ( ). The Comment view displays any descriptive…

Circular view

Windows, Views, Panels and Tools » Document window views » Circular view

The Circular view is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Circular tab ( ). The Circular view is only available for…

Linear view

Windows, Views, Panels and Tools » Document window views » Linear view

The Linear view is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Linear tab ( ). The Linear view is only available for…

Annotation Results Window

Plasmid Auto-Annotation » Perform the auto-annotation procedure » Annotation Results Window

The Annotation Results window displays putative matches between SeqBuilder Pro’s plasmid Feature Library and one or more query sequences, usually vector sequences from a cloning project. If the query sequence lacks some/all of the located features from the…

Primer Design view

Windows, Views, Panels and Tools » Document window views » Primer Design view

The Primer Design view is one of the ten is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. It also has its own set of tools. To make it the active view (or one of two active views), click on the…

Site Summary view

Windows, Views, Panels and Tools » Document window views » Site Summary view

The Site Summary view is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Site Summary tab ( ). The Site Summary view is only…

BLAST Search Results window

Open an Existing Sequence » Open a sequence from an online database » Open a BLAST database file using a similarity search » BLAST Search Results window

When a BLAST database search is complete, the BLAST Search Results window appears, showing a list of sequences that match your query. Task Button to use… To open one or more results in the selected Lasergene application Open…

ORFs

To display open reading frames (ORFs) in the Linear or Sequence views: Click on the Translations and ORFs tool ( ) and make a selection from the ORFs sub-menu. Displayed ORFs appear as color-coded boxes and lines. Multiple ORFs can be displayed on the same…

Site-Directed Mutagenesis

Site-directed mutagenesis is a molecular biology method that is used to make specific changes to the DNA sequence of a gene. As of Lasergene 16.0, you can perform site-directed mutagenesis using Protean 3D’s Protein Design service together with SeqBuilder Pro.…

Primers

SeqBuilder Pro lets you design primers for regions of interest on your sequence. The following video is a brief overview of SeqBuilder Pro’s primer design workflow. To learn more about working with primers, see: Create primer pairs automatically Create…

Feature Library Manager

Plasmid Auto-Annotation » Create a custom feature database for auto-annotation searches » Feature Library Manager

The Feature Library Manager is a browser for the over 150 entries in SeqBuilder Pro’s built-in plasmid Feature Library, and allows you to add your own features to the database. This window also lets you specify the appearance of features in the Annotation…

Primers view

Windows, Views, Panels and Tools » Document window views » Primers view

The Primers view is one of the ten views available in the Document window, and shares a sub-set of button tools with the other views. To make it the active view (or one of two active views), click on the Primers tab ( ). The Primers view is available for…

Print on Windows

Copy, Print, Save and Export » Print on Windows

To print from within SeqBuilder Pro on Windows: Select File > Print or the keyboard shortcut Ctrl/Cmd+P or use File > Print Preview (see below) and select the Print tool. Select a printer and choose the pages and quantities to print. To view a preview before…

Create and manage individual enzymes

Enzymes » Create and manage individual enzymes

The Enzyme Manager allows you to create, modify or delete enzymes for use in SeqBuilder Pro or other Lasergene applications. If you want to create a new enzyme, open the manager using Enzymes > New Enzyme. To edit an existing enzyme, select the enzyme in a view and…

Close and Exit

To close a single project: Select File > Close or use the keyboard shortcut Ctrl/Cmd+W. To close all projects and leave SeqBuilder Pro: Windows: Select File > Exit Macintosh: Select SeqBuilder Pro > Quit. If you are closing a project that has been edited since…

Open an Existing Sequence

SeqBuilder Pro is so powerful that you can import the entire human genome or as many as 5,000 bacterial genomes into a single SeqBuilder project file (.sbp). The following topics describe three ways to open an existing sequence: Open a file stored on your…

Change the default application for opening Lasergene files

Open an Existing Sequence » Open a local sequence » Change the default application for opening Lasergene files

On Windows: Open the Control Panel. Go to Programs > Default Programs > Associate a file type or protocol with a specific program. Select extension you wish to change in the Extensions list and then click the Change program button. Click the Browse…

Option C – Use an entire open SeqBuilder Pro sequence as the insert

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option C – Use an entire open SeqBuilder Pro sequence as the insert

Use File > Open to open the file or SeqBuilder Project (.sbd) containing the insert. From the Cloning menu, select one of the following commands: Gibson, LIC Cloning; In-Fusion Cloning, GeneArt Cloning; MultiSite Gateway Pro Cloning; Gateway Expression Clone;…

Print on Macintosh

Copy, Print, Save and Export » Print on Macintosh

To print from within SeqBuilder Pro on a Macintosh: Select File > Print or the keyboard shortcut Cmd+P. Initially, an abbreviated version of the Print dialog is displayed. To view all print options, press Show Details. Once expanded, the selection you make in the…

Try it! – Open an Entrez sequence by accession number

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…

Step 7: View and print cloning results

Automated Virtual Cloning » Step 7: View and print cloning results

The Cloning Summary provides details about the components of the cloning simulation, including fragment inserts, primers, and the steps needed to prepare the vector and amplify inserts. It also displays the reading frame around all fragment junctions graphically,…

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…

Option E – Use the PCR product of the current primer pair as the insert

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

If you will be using the TA cloning method, you can use the PCR product of the current primer pair as an insert. Use File > Open to open the file or SeqBuilder Pro project (.sbd) containing the sequence of interest. Create primer pairs. With the Primer…

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! – 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…

Choose the genetic code

Translations » Choose the genetic code

To select a genetic code to use in translations: Select Sequence > Select Genetic Codes. The active genetic code is preceded by a check mark. Click on a code to select it. The default genetic code used is the Standard Genetic Code. If prompted, navigate to…

Available cloning methods

Automated Virtual Cloning » Step 2: Specify the method and options » Available cloning methods

SeqBuilder Pro supports the following cloning methods: 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…

Markers panel

Windows, Views, Panels and Tools » Document window panels » Markers panel

The Markers panel, represented by a ladder icon, lets you choose which molecular weight marker to apply to a lane in the Gel Simulation view. The Markers panel becomes available only after you initiate an agarose gel simulation using the File > New Agarose Gel…

Features

Features are annotations made to a specified range on a sequence. They can be imported as part of a sequence file (e.g., Genbank, EMBL, etc.), or they can be created within SeqBuilder Pro. See the following topics to learn how to: Create or delete features Edit…

Try it! – PCR-directed restriction cloning

Automated Virtual Cloning » Try it! – PCR-directed restriction cloning

This tutorial demonstrates how to cut and clone a signal transduction gene into the pENTR/D-TOPO vector. 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…

Enzymes panel for gels

Windows, Views, Panels and Tools » Document window panels » Enzymes panel » Enzymes panel for gels

A specialized version of the Enzymes panel becomes available after you use File > New Agarose Gel to initiate an agarose gel simulation. It can be opened by clicking on the Enzymes tab, represented by a scissors icon () and located to the right of the Gel Simulation…

Primers panel

Windows, Views, Panels and Tools » Document window panels » Primers panel

The Primers panel, represented by a green/red arrow icon, lets you choose which primer pairs to apply to a lane in the Gel Simulation view. The Primer panel becomes available only after you initiate an agarose gel simulation using the File > New Agarose Gel command.…

Fragment Sizes view

Windows, Views, Panels and Tools » Document window views » Fragment Sizes view

The Fragment Sizes view is available in the Document window after using the File > New Agarose Gel command. The view initially appears empty, or may contain one or more faintly outlined boxes. After setting up an agarose gel simulation, the view is populated with…