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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…
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…
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)
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…
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 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…
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…
Copy, Print, Save and Export
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
Welcome to SeqBuilder Pro
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…
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…
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! – 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…
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,…
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…
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…
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 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…
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…
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…
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…
Agarose Gel Simulation
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…
Translations
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
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,…
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…
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 Virtual Cloning
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…
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 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…
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:…
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,…
Plasmid Auto-Annotation
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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,…
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…
ORFs
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…
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…
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…
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…
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…
Automated Batch Cloning
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…
Primers
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…
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…
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…
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…
Site-Directed Mutagenesis
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.…
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…
Use preset layouts or create new ones
Customize the Sequence Display » Use preset layouts or create new ones
The following table discusses use of menu commands that affect the layout of a sequence in the Document window. Task How to… To choose a template and apply it to the current file Choose View > Apply Layout. To save the current…
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…
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…
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…
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…
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.…
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…
Show or hide features
Features » Show or hide features
To choose which features to show/hide: In the Show column of Features view, rows with check marks represent the features currently displayed in the graphical views. Rows without check marks are not displayed in the views Click the Show column for a particular row to…
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…
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…
Change the rendering style or font
Customize the Sequence Display » Change the rendering style or font
To change the rendering style or font of a selected feature, enzyme or range: Open the Style panel and perform one of the tasks in the table below. Task How to… To show/hide an outline around a selected item To show/hide an outline,…
Choose, show or hide primers
Primers » Choose, show or hide primers
To choose a selected primer pair (i.e. make it the active pair): Within the Primers view, select a primer pair and choose Priming > Set as Active Primer. The selected primer pair will be opened in the Primer Design view, where it can be edited or analyzed. To…
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’…
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…
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…
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…
Settings panel for other situations
Windows, Views, Panels and Tools » Document window panels » Settings panel » Settings panel for other situations
*Note: When performing an agarose gel simulation, the Settings panel has different options, which are described in Settings panel for gels. The Settings panel, represented by a gear icon ( ), is located on the right of the Document window and lets you display or hide…
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…
Step 6 (optional): Verify the clone
Automated Virtual Cloning » Step 6 (optional): Verify the clone
SeqBuilder Pro 15.1 and later offers the ability to verify whether or not a clone produced in the laboratory matches the version designed in SeqBuilder Pro. To learn how, watch this brief video or follow the written instructions below: To verify a clone: Use…
Document window panels
Windows, Views, Panels and Tools » Document window panels
The right side of the Document window consists of four panels: Style, Enzymes, Settings and Details. To display/hide the panels: Choose View > Show/Hide Side Panels or use the Show/Hide Settings tool () on the left of the Document window. To move a panel from the…
Use editing commands
Create a New Sequence » Use editing commands
The following editing commands can be used in multiple views, panels and dialogs. Task How to… To remove the current selection from the project and place it on the clipboard Choose Edit > Cut or use keyboard shortcut Ctrl/Cmd+X. Among…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
Customize the Sequence Display
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…
Motion Library
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 a New Sequence
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:…
Step 3: Specify the vector and entry clone
Automated Virtual Cloning » Step 3: Specify the vector and entry clone
After specifying the cloning method and options, the next step is to choose the vector. In addition, if you are performing Gateway Expression cloning, you will need to specify which previously-saved Gateway Entry clone to use. From the Clone tab of the Project…
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…
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…
Pentamer profile
Primers » Methods used in primer design » Pentamer profile
Pentamer free energy is one of the most important considerations in designing good primers. To perform well a primer needs to have low stability at the 3’ end (usually higher than -8.5 kCal/mol) and higher stability toward the 5’ end. This will help to…
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)…
Rulers
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…
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,…
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…