Search - User Guide to SeqBuilder Pro

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…

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 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…

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:…

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…

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…

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:…

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…

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,…

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…

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…

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…

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 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…

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…

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…

Customize the Sequence Display

To specify sequence characteristics and how a sequence is displayed: Task How to… To add, delete, or change the letters in a sequence Open the Sequence view and insert the cursor where desired. Delete letters, type in new letters, or…

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. …

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…

View cut sites and recognition sequence

Enzymes » View cut sites and recognition sequence

In the Sequence and Primer Design views: To show cut sites, click and hold on a restriction enzyme label. Cut sites are represented by thin blue lines. To display the recognition sequence, press the Alt (Win) or Option (Mac) key while clicking and holding on an…

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

Option B – Copy inserts from another SeqBuilder Pro cloning project

Automated Virtual Cloning » Step 1: Start a cloning project and specify the insert » Option B – Copy inserts from another SeqBuilder Pro cloning project

Open an existing SeqBuilder Pro cloning project that has the desired inserts in its Inserts folder. Press File > New Cloning Project. Drag the inserts from the original project’s Inserts folder into the new project’s Inserts folder. Close 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…

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;…

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…

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…

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…

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…

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…

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…

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…

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…

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’…

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”…

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…

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…

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…

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…

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…

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…

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…

Specify URLS for BLAST and Entrez Searches

Open an Existing Sequence » Open a sequence from an online database » Specify URLS for BLAST and Entrez Searches

To specify URLs to use for online database searching : Depending on your Lasergene version, choose Edit > Preferences or Settings (Windows) or SeqBuilder Pro > Preferences or Settings (Mac). Select the Servers tab. The upper and lower portions of this dialog let you…

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…

Motion Library

Lasergene applications are designed to work together seamlessly. One useful workflow is to create or edit a protein sequence in SeqBuilder Pro, fold it in Novafold and view the finished product in Protean 3D. Whether or not you are already licensed to use Protean 3D,…

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…

Turn off usage logging

Appendix » Turn off usage logging

By default, usage logging is enabled for Lasergene. To opt in/out of usage logging: Launch the DNASTAR Navigator. Use whichever of the following commands is available; the command varies by Lasergene version and operating system. Window > Preferences…

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…

Features view

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

The Features 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 Features tab ( ). The Features view displays a table of…

Enzyme Selector Manager

Enzymes » Create and manage sets of enzymes » Enzyme Selector Manager

The Enzyme Selector Manager is opened by choosing Enzymes > New Selector or Enzymes > Selector Manager. This topic describes the layout of the Manager. Additional information about using the Manager is in the topic Create and manage sets of enzymes. The…

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…

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…

Modify the genetic code

Translations » Modify the genetic code

To modify and rename a genetic code: Open a sequence or SeqBuilder Pro project. Select Sequence > Edit Genetic Code. The two-tabbed Genetic Code Editor appears. ————- Task How to… To assign a name for the…

Document window views

Windows, Views, Panels and Tools » Document window views

The following video contains a short tour of each of the Document window views: To change from one view to another: Click the tab with the name of the desired view. By default, the upper portion of the window lets you choose any of 1-4 views, depending…

Rulers

To display or hide rulers: Use the Rulers tool ( ). You can also hide a specific ruler by right-clicking on it and choosing whichever command is available: Hide Ruler or Hide Translation Ruler. Rulers can only be edited in the circumstances described below: To…

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.…

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…

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…

Copy 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 » Copy search results

Selected results may be copied to the clipboard from the Entrez or BLAST Search Results windows. To copy detailed information: 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…

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…

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…

Shared button tools

Windows, Views, Panels and Tools » Shared button tools

The Document window features a set of shared button tools. Tools apply to the currently-active view, and different subsets of the tools are available for different views. By default, the shared button tools are located on the left side of the window. However, the set…

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…

Minimap view

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

The Minimap 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 Minimap tab ( ). The Minimap view is available only for…

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,…

Example of showing potential cuts at ambiguous bases

Enzymes » Show or hide enzymes in other views » Example of showing potential cuts at ambiguous bases

The following example shows the use of the Show Potential Cuts at Ambiguous Bases option, located in the Enzymes panel: Create a new DNA project and paste in the following sequence, which contains many ambiguous…

Primer Design tools

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

The following tools are located in the upper right of the Primer Design view: Tool Description Selection Mode To enable selection of a region of sequence using the mouse. After selecting this tool, click on a translated amino acid to select…

Change the way enzymes are displayed

Enzymes » Change the way enzymes are displayed

To change the way that enzymes appear on a particular view: Description Command To position the label parallel to the sequence (default). Format > Horizontal Labels To position the label perpendicular to the sequence. Format…

Show or hide enzymes in other views

Enzymes » Show or hide enzymes in other views

To show/hide sets of enzymes using the Enzymes tool: To apply groups of enzymes to the sequence based on the frequency of cuts, type or class, site complexity, or overhang compatibility, click the Enzymes tool ( ) and make a selection from the list. Choosing None…

Create or delete features

Features » Create or delete features

To create a new feature: Within any Document window view that permits range selection, select a range of the sequence. To select a range that wraps the origin, position the cursor at one end of the feature, and then use Ctrl/Cmd+Shift+Click to select the other end…

Select an Object or Range

Create a New Sequence » Select an Object or Range

When you select an object or range in one SeqBuilder Pro view, the selection is made in all other applicable views simultaneously. To select an object in any SeqBuilder Pro view: Click the object (e.g., a feature, translation, enzyme, ruler, etc.). To select a…

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…

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…

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…

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…

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…

Join feature segments

Features » Join feature segments

To join a new segment to an existing feature: (optional) If an initial feature segment doesn’t exist, create one. Select a region of a sequence to join to the existing feature. Select Features > Join to Feature. The Join to Feature dialog appears. This…

Windows, Views, Panels and Tools

The Document window opens when you open a nucleotide or protein sequence or a SeqBuilder (.sbd) document. This is the window where you can edit the sequence or add/edit features, restriction enzymes, ORFs, translations and/or rulers to the sequence. On the left of…

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…

Move an object or row

Customize the Sequence Display » Move an object or row

To move an object in the Circular, Linear, or Sequence views: Double-click on an object and then drag it in the desired direction. To move a row: Change the order of rows in a tabular view by dragging the identifying character at the left of the row up or down with…

SeqBuilder Pro Tutorials

SeqBuilder Pro tutorials are typically located in the table of contents just under the help topic they are designed to illustrate. For convenience, all tutorials are also listed below. Primer tutorials: Create and modify primers for TA cloning Cloning…

Create and manage sets of enzymes

Enzymes » Create and manage sets of enzymes

Enzyme selectors provide a way to define a group of restriction enzymes based on specific criteria. Once created, the selector will appear in the list of preset enzyme categories that appears when you click the Enzymes tool ( ).Once defined, enzyme selectors are…

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…

Details panel

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

The Details panel, represented by a blue “information” icon ( ) displays information about an active view or selection in the Document window. The Details panel can be opened by clicking on the Details tab. If the tab is hidden, reveal it by clicking the Show/Hide…