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Tracks panel
GenVision Pro Interface » Panels » Tracks panel
The Tracks panel lets you manage tracks displayed in the views. To open this panel, do either of the following: Click on the Tracks tab (). Use the View > Tracks > Tracks command. The uppermost part of the Tracks panel lets you specify which tracks are…
Ruler tracks
Work with Tracks » Ruler tracks
One or more Ruler tracks can be added to the Overview header and/or to the Analysis view header or footer. For detailed information about applying tracks, see Work with Tracks. These are the Track panel items to check if you want to display one or both Ruler…
Feature tracks
Work with Tracks » Feature tracks
One or more Feature tracks can be added to the Overview and/or to the Analysis view header or footer. Feature tracks may come from the sequences in an assembly, or can be imported separately using File > Add Track. For detailed information about applying tracks, see…
Sashimi tracks
Work with Tracks » Sashimi tracks
Analysis of mRNA isoform expression is a key aspect of understanding gene expression. For many genes, the change in isoform ratios for a given gene produce a more significant physiological effect than the overall expression level of that gene. Isoforms are typically…
Reads tracks
Work with Tracks » Reads tracks
If you are viewing an assembly created in SeqMan NGen, you can add a track to the Analysis view showing each of the aligned reads in the selected experiment. For detailed information about applying tracks, see Work with Tracks. This are the Track panel items to check…
Add tracks
Add Data » Add tracks
A data track in BED file (.bed), GenVision box file (.txt) or Wiggle (.wig) format can be imported into a GenVision session. To add tracks: Do any of the following: Drag & drop one or more track files (see above) on an open GenVision Pro session Use the…
Coverage tracks
Work with Tracks » Coverage tracks
If data are available, you can choose to display a numeric track in the body of the Analysis view. As of Lasergene 17.3, the main numeric track type is the Coverage track. For detailed information about applying tracks, see Work with Tracks. This is the Track panel…
Work with Tracks
Work with Tracks
Tracks are rows of information pertaining to a header, footer, or individual sequence row in certain GenVision Pro views. Tracks may be displayed or hidden by check or unchecking boxes in the Tracks panel. The following tracks can be applied, removed or (in some…
Rename Assemblies and Tracks
Rename Assemblies and Tracks
A selected assembly or track can be renamed manually or by using specified data fields. See the following topics for details: Create names automatically using specified data fields Rename a single sequence manually
When multiple tracks are selected
GenVision Pro Interface » Panels » Details panel » When multiple tracks are selected
If two or more tracks have been selected in the Overview or Analysis view, the Details panel contains the following information. Heading The heading contains: The number of tracks currently selected (in blue). Summary – Description of…
Part B: Work with feature tracks
GenVision Pro Tutorials » Try It! – Analyze an E. coli assembly » Part B: Work with feature tracks
Features are displayed as colored arrows in the Overview and the Analysis view. In this part of the tutorial, you will learn to toggle between displaying/hiding features, and to view features that are not currently visible. To see an information balloon for any…
Part D: Work with region tracks
GenVision Pro Tutorials » Try It! – Analyze an E. coli assembly » Part D: Work with region tracks
In this part of the tutorial, you will load two BED files associated with the E. coli assembly. MG1655_m56_v3.prophage-regions.bed. contains ten regions or intervals corresponding to the locations of prophages within the genome of this particular strain…
Options section
GenVision Pro Interface » Panels » Tracks panel » Options section
The Options section is used to edit settings for the track type currently selected in the Tracks panel, and varies in appearance depending upon the selection. Access the Options section by clicking on the Tracks panel expand bar entitled Options or by choosing View >…
Layout section
GenVision Pro Interface » Panels » Tracks panel » Layout section
The Layout section lets you change the height of a track and the space above and/or below a track. Changes made in this section are applied to all currently selected tracks. Access this section by clicking on the Tracks panel expand bar entitled Layout, or by choosing…
Overview
GenVision Pro Interface » Views » Overview
The Overview shows an overview of the currently-selected chromosome (in the Genome view) and its features. To access the view, click on the Overview tab (the dark blue part of the image, below) or use View > Overview > (Name) > Show. This view was released in…
Details panel
GenVision Pro Interface » Panels » Details panel
The Details panel shows details of the application, selection or session. Details are available for all tracks in the Overview and Analysis view, as well as the Tracks panel. To open this panel, do any of the following: Click on the Details tab (). Use the…
Reference track
Work with Tracks » Reference track
If you are viewing a templated assembly, you can choose to display a Reference track in the Analysis view header or footer. For detailed information about applying tracks, see Work with Tracks. This is the Track panel item to check if you want to display a Reference…
GenVision Pro Interface
GenVision Pro Interface
The following table describes components of the GenVision Pro user interface, along with links to more in-depth information about each item: Item Description Menus The GenVision Pro menus are: GenVision Pro (available only on…
When one track is selected
GenVision Pro Interface » Panels » Details panel » When one track is selected
If a single track has been selected in the Overview or Analysis view, the Details panel contains the following information. Heading The heading contains: Type of track or assembly name, in blue. Summary – Basic information about what…
Panels
GenVision Pro Interface » Panels
Settings panels allow you to optimize the look, contents and layout of the GenVision Pro view. To learn what can be done within each panel and their “areas” (expandable sections within each panel), click the links…
Add Data
Add Data
Once you have created a GenVision Pro session, the next step is to add data. To add this type of data… …see this topic Where data type appears in GenVision Pro How to view the data .assembly files created in SeqMan NGen …
Open an existing session
Create or Open a Session » Open an existing session
To open an existing GenVision Pro (.gvp) session : Do any of the following: From the Welcome screen, click the Open tab, then click on Open session. From the Details panel, click the link Open a session. Use the File > Open command. Press Ctrl+O…
Export the consensus sequence
Export » Export the consensus sequence
To export a consensus sequence: From the Tracks panel, check the boxes pertaining to read tracks. In the Analysis view, select a read track. A toolbar pops up at the track’s top left corner. Click the Export data tool (). The Export Consensus popup…
Use Basic Editing Commands
Use Basic Editing Commands
The following basic editing commands are available in GenVision Pro: Command Keyboard Shortcut Right-Click Option Description Edit > Cut Ctrl/Cmd+X Cut This command is not enabled in GenVision Pro. Edit >…
Analysis view
GenVision Pro Interface » Views » Analysis view
The Analysis view shows tracks for a single sequence. The view is empty unless the session contains only one sequence; or until a single sequence has been chosen in the Overview or by using the navigation tools or Places panel bookmarks. At that point, the Analysis…
Customize the Look and Layout
Customize the Look and Layout
The following topics describe the many ways you can customize the look and layout of GenVision Pro. Use the Style panel to change the look of a view (font styles and sizes, colors, number of decimal places, etc.) Customize the appearance and layout of…
Features panel
GenVision Pro Interface » Panels » Features panel
The Features panel lets you specify which feature types should be visible in the Overview and the Analysis view when the feature and region tracks are visible. To open this panel, do any of the following: Click on the Features tab (). Use the View > Features…
When a non-empty session is open
GenVision Pro Interface » Panels » Details panel » When a non-empty session is open
If a session is open and data has been added, the Details panel contains the following information: Heading The session file name, in blue. Sequences * Sequences – Number of sequences in the assembly. * Sequence type…
Edit an exported image in PowerPoint
Export » Export an image of a view » Edit an exported image in PowerPoint
The following video shows how to edit exported images of your alignment or genomic tracks within Microsoft PowerPoint:
Experiments section
GenVision Pro Interface » Panels » Explorer panel » Experiments section
The Experiments section is a section in the Explorer panel. This section lists any .assembly files already loaded into the current GenVision Pro session and allows you to add additional files or delete existing ones. Some of the data added here as part of an .assembly…
Overview section
GenVision Pro Interface » Panels » Style panel » Overview section
The Overview section contains options affecting the Overview. To access this section, click on the Style panel expand bar entitled Overview, or choose View > Style > Overview. Customization for font style and size applies to all text in the Overview. Individual…
Part C: Investigate sequence coverage
GenVision Pro Tutorials » Try It! – Analyze an E. coli assembly » Part C: Investigate sequence coverage
GenVision Pro’s navigation tools consist of a “sequence selector,” a text box, and a Go button. In this part of the tutorial, you will use the navigation tools to go to a particular region of low coverage that begins around 4,314,000. In the navigation…
Button tools
GenVision Pro Interface » Button tools
At the top of the GenVision Pro window are eight button-style tools, as well as a set of navigation tools. In the bottom right corner of each view, GenVision Pro offers two additional button-style tools for selecting the screen mode. You can toggle between…
Make a Selection
Make a Selection
Within the Analysis view, you can select an entire chromosome, a portion of one, or a specific portion of chromosome corresponding to a feature. The active selection is highlighted in light blue. The selection can then be copied to the clipboard in standard or FASTA…
Pairwise view
GenVision Pro Interface » Views » Pairwise view
After the Jobs panel shows the Status of a BLAST search or Entrez search is Done, pressing the “Done” hyperlink opens the search results simultaneously in the Text, Table, and Pairwise views. All three views are contained in a large pop-up window that is…
Add genomes from NCBI
Add Data » Add genomes from NCBI
To import a genome from the National Center for Biotechnology Information (NCBI) database via organism name or accession number: Choose File > Download and Add Genome or press the Download and add a genome to the session button to (). In the Download Genome…
Part A: Start a new session and rename a sequence using data fields
GenVision Pro Tutorials » Try It! – Analyze an E. coli assembly » Part A: Start a new session and rename a sequence using data fields
In this first part of the GenVision Pro tutorial, you will start by downloading and extracting the tutorial data from the DNASTAR website. Next, you will begin a new session and add an E. coli assembly produced by DNASTAR’s SeqMan NGen. You will then create a…
Customize the appearance and layout of views
Customize the Look and Layout » Customize the appearance and layout of views
The following table lists ways in which you can customize the appearance and layout of views. Task How to… Show a view Use View > (View Name) > (chromosome or contig number) > Show. The third item in the command at left may or may not…