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Edit primers
Primers » Edit primers
There are several ways to edit a primer in the Primers view or the Primer Design view: Modify a base in the primer Modify the primer length Introduce a codon change or mutation Introduce restriction sites
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…
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…
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…
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…
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…
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…
Style panel
Windows, Views, Panels and Tools » Document window panels » Style panel
The Style panel, represented by a paint roller icon ( ), provides the ability to change the appearance of a currently selected item in the Document window. Open the Style panel using any of these methods: Click on the Style tab to bring that panel to the…
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…
Windows, Views, Panels and Tools
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…
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…
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,…
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…
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…
Features
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…
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,…
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…
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 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)…
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…
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…
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…
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…
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.…
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…
Introduce restriction sites
Primers » Edit primers » Introduce restriction sites
To introduce restriction sites for primers: Create or import primers or primer pairs. From the Primer Design view, either click on the Introduce Restriction Site tool ( ) at the top left of the window, or choose Priming > Introduce Restriction Site. Click…
Delete primers
Primers » Delete primers
To delete a primer or PCR product: Open the Primers or Primer Design view. Select the corresponding feature and select Features > Delete or Edit > Delete Feature. Or right-click on the feature and choose Delete or Delete Feature from the context…
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…
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…
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…
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…
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 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:…
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…
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…
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…
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…
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.…