DNASTAR - Lasergene SeqBuilder - Sequence editing, Annotation and Cloning

SeqBuilder - NEW Features Added in version 8.0

» Printable PDF overview for SeqBuilder

» View tutorial Training videos of SeqBuilder and other Lasergene modules

Sequence editing, mapping, annotation, and automated virtual cloning

SeqBuilder enables you to edit nucleic acid and amino acid sequences and view the sequences and related items in multiple ways. SeqBuilder's window can be split into multiple panes so that more than one view can be displayed at any time. The possible views include a residue-specific view, a linear map, a circular map, a compact map of restriction cut sites (mini map), as well as a list of features, a summary of all restriction cut sites, and any comments. Each view lists a number of items that can be individually turned on or off including features, restriction sites, translations in all six reading frames, ORFs, and rulers. Many of these items can also be positioned and modified to emphasize certain characteristics. Dynamic links between the sequence and its annotations automatically update feature coordinates when you edit a sequence. Available functionality also includes the ability to reverse complement, translate, back-translate sequences, identify ORFs and perform BLAST and Entrez text* searches directly to NCBI.

A New Feature added with Lasergene v8.0 permits users to design primers directly in SeqBuilder. In general, the task of primer design in SeqBuilder is focused on the specific task of creating a PCR insert from a region of interest. Typically, this task involves several steps as shown below:

Identify the region of interest, usually containing a gene.
Create primer pairs near the ends and in the same reading frame as the gene.
Select one pair from the search results in the Primer Design or Primer List view.
Modify the primers as desired.
Cutting and cloning the insert into a vector.

The image illustrates the Primer Design View with Design Toolbar, the Residue Pane, the Mispriming Pane and the Alternate Pairs Pane

SeqBuilder's editing capabilities are also integrated into many other Lasergene modules. Edits made in SeqBuilder will be shared automatically with other Lasergene applications that are analyzing the same data, making SeqBuilder an integral member of the powerful Lasergene suite.

SeqBuilder Features

Create a New Cloning Project by adding (cut and paste) the insert you wish to clone
Select the method you wish to follow and the software will provide the appropriate vector selection from the Lasergene Vector Catalog
Add your own Vectors to the Vector Catalog
The Cloning Wizard will provide help if the ends to be cloned are not compatible
The wizard will construct the Virtual clone automatically once the ends and the vector selected are correct

View sequences in a variety of forms including graphically rich circular and linear displays
Split the window to display multiple views of the same sequence simultaneously
Customize graphical and textual displays through simple curtain and click-and-drag interface
- Create, design and move graphic annotations
- Create default displays for specific types of annotations
- View double-stranded or single-stranded DNA, RNA or amino acid sequences
Create single page maps or multi-page posters
Interpret and display Genbank features graphically
Display lists of features, summary of cut sites and sequence comments
Display and save concise summaries of restriction sites sorted by classification
Copy and paste high-quality, resizable pictures into other software applications

Share sequence and feature edits simultaneously across multiple Lasergene modules
Open and save project files from GeneQuest, MegAlign, Protean and PrimerSelect

Create or edit constructs through standard editing and enhanced copy/paste functions
View ORFs that are updated with every sequence edit
Translate DNA or back translate protein using any of the supplied genetic codes or customize your own
Choose restriction sites to display based on any combination of:
- Manual selection of enzymes
- Frequency of cuts
- Type or class of enzyme
- Site complexity
- Overhang compatibility
Find related sequences using the integrated BLAST and Entrez* search tools
Edit the sequence, then the feature coordinates will update automatically

Import data from many popular file formats
Batch import Vector NTI files retaining feature names
Export data into the original file format automatically when the file format is one of several exportable formats offered
Download sequences directly from NCBI* using accession numbers, BLAST, or text searches

* Requires Internet Connection

» Printable PDF overview for SeqBuilder

» View a video tutorial of SeqBuilder

Manage vectors, inserts, clones, and other sequences in project files

Automated virtual cloning for three protocols

View the sequence, ORFs, translations

Restriction site summary view and enzyme manager

Alter the display in many views, like this linear view

Restriction site summary view and enzyme manager

Primer Design table in SeqBuilder

Display as a circular map