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Related topics are listed below.
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…
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…
Make a session active
Create or Open a Session » Make a session active
To make a session active: Do any of the following: Click+ on any session tab to make that session active. Click on the Window menu and choose the name of the session from the list. Press Ctrl+; (Win) or Cmd+; (Mac) to open a “session chooser.”…
Create a new session
Create or Open a Session » Create a new session
To create a new, untitled GenVision Pro session : Do any of the following: From the Welcome screen, choose New session to open a new blank session; or Add assemblies to new session to open a session and add sequences at the same time. From the Details panel,…
Export data to a file
Export » Export data to a file
Data can be exported using the Export data tool () located in the top right of some GenVision Pro views and panels. The table below shows export options available from each view, as well as menu commands that can be used to export aligned sequences or the consensus…
Create or Open a Session
Create or Open a Session
Because GenVision Pro does not store data when you close it, the information shown in the interface is called a “session,” rather than a “project.” Once you open GenVision Pro, you can open one or many sessions. Each session is displayed in a…
Filter a single-sample Variants view
Explore Variants and Structural Variations » Analyze variants in a single sample » Filter a single-sample Variants view
When a single-sample Variants view is active, you can open a filter dialog to specify which variants are shown in the table. To open the Variant Filter Criteria dialog, use the Variants > Filter command, press the Filter tool () in the upper-right of the view, or…
Analyze variants in a single sample
Explore Variants and Structural Variations » Analyze variants in a single sample
The sections below describe how to create and modify the single-sample version of the Variants view. For information on a version of the view that supports multi-sample variant comparison, see Compare variants across samples. These two versions of the view appear…
Launch a session from within ArrayStar
Create or Open a Session » Launch a session from within ArrayStar
To view and analyze a selected entry from ArrayStar: Create or open a project in DNASTAR’s ArrayStar application. Open any table and locate a row with a position of interest. Select the row and choose File > Send Selection To > GenVision Pro or right-click…
Export an image of a view
Export » Export an image of a view
GenVision Pro lets you export an image of the Overview or Analysis view for use in a text editor or similar program. Do either of the following: Press the Export image tool () in the upper right corner of the view you want to export. Use File > Export…
Rename a single experiment, track, or chromosome
Rename Experiments, Tracks, or Chromosomes » Rename a single experiment, track, or chromosome
This topic describes how to manually rename an individual experiment, track, or chromosome. These new names are used solely within the GenVision Pro application. (Note: to instead name items using specified data fields, see Creating names automatically using…
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 a subset of the following information: Heading The session file name, in blue, followed by the sequence type (DNA, RNA, protein). Sequences Sequences –…
Create a new assembly using SeqMan NGen
Create or Open a Session » Create a new assembly using SeqMan NGen
To create a new assembly from within the GenVision Pro application, do either of the following: From the Welcome screen, click the New tab on the left and then choose New assembly with options on the right. From within a GenVision Pro session, click on the New…
Filter a multi-sample Variants view or set
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set
When you filter a multi-sample Variants view, or use the Variants > Create a Set of Variants > With Filter command to create a filtered set of variants, a multi-screened wizard opens. In the former case, the wizard has five screens and is called the “Filter…
Create a new variants set based on existing sets
Explore Variants and Structural Variations » Create and analyze variant sets » Create a new variants set based on existing sets
GenVision Pro lets you create a new variants set based on the presence/absence of variants in sets that were previously created. Before following any of the procedures below, you must first select two or more existing variants sets in the Variant Sets section of the…
When a region or one structural variation is selected
GenVision Pro Interface » Panels » Details panel » When a region or one structural variation is selected
When a portion of a sequence has been selected in the Analysis view (e.g., by double-clicking on a feature, or by dragging across the sequence with the mouse), or when a single structural variation is selected in the Structural Variation view, the Details panel…
When no session, or a blank session, is open
GenVision Pro Interface » Panels » Details panel » When no session, or a blank session, is open
When no session, or only a blank session, is open, the Details panel displays links to help you get started in GenVision Pro. Click on the links to: Create or open a session Add assemblies or BAM alignments to the session Watch a training video on…
Save a custom layout and apply it to other projects
Customize the Look and Layout » Save a custom layout and apply it to other projects
You can change the layout of GenVision Pro’s views and panels as described in Customize the look and layout. Once you have arrived at a layout you like, you can save it and then apply it to future projects, either by default or only when you specify that it be…
Troubleshoot the error “A different version is running”
Appendix » Troubleshoot the error “A different version is running”
If you receive the error “A different version of Lasergene is running” when you try to launch a Lasergene application, but another version of Lasergene actually isn’t running, there may be a lingering .state file from another version that needs to be…
Search Within the Project
Search Within the Project
To navigate to a specific position: Do any of the following: Open the Places panel and double-click on a previously-stored location. Use Edit > Go to Place or press Ctrl/Cmd+J. In some cases, the right-click option Go to Place may also be available. In the Go…
Analysis view
GenVision Pro Interface » Views » Analysis view
The Analysis view shows tracks for a single sequence. The view is empty or cannot be opened at all unless the session contains only one sequence; or until a single sequence has been chosen in the Overview or Explorer panel, or by using the navigation tools or Places…
Overview
GenVision Pro Interface » Views » Overview
The Overview shows an overview of the chromosome currently selected in the Genome view and its features. To access the view for the first time in a session, select a row in the Chromosomes section and click the Show overview of selected chromosomes tool (). Once the…
Set temporary file preferences
Appendix » Set preferences » Set temporary file preferences
GenVision Pro creates and uses temporary files while a session is open. The need for temporary file space grows with the number and length of the sequences and track data in open sessions. If you expect the temporary files will be too large to fit in the default…
Recent section
GenVision Pro Interface » Panels » Places panel » Recent section
When you perform a search for a gene, feature or numerical sequence location using the navigation tools or the Edit > Go to Place command, each found location is automatically stored in the Recent section of the Places panel. Access this section by clicking on the…
Navigation tools
GenVision Pro Interface » Navigation tools
GenVision Pro’s navigation tools are located just to the right of the button tools and consist of a “sequence selector” (the drop-down menu), a text box, a Go button, and two green arrows. By default, (Genome) is shown in the sequence selector, causing the entire…
Region capture tracks
Work with Tracks » Region capture tracks
If you created an exome or gene panel assembly in SeqMan NGen using a BED file with targeted regions, GenVision Pro lets you display a Region track in the Overview and/or Analysis view. To display the Regions track, check the associated checkboxes in the Tracks panel.…
Received section
GenVision Pro Interface » Panels » Places panel » Received section
After opening a SeqMan NGen assembly in DNASTAR’s ArrayStar application, you can send up to 100 data rows from its Gene Table or SNP Table directly to GenVision Pro using the File > Send Selection To > GenVision Pro command. When you do this, each row exported…
Favorites section
GenVision Pro Interface » Panels » Places panel » Favorites section
The Favorites section is similar to the bookmarks folder for a web browser. It contains a list of previously-visited locations that you have decided you may wish to visit again. Favorites are listed in the same order in which they were added, by default, though you…
Customize the layout of other window components
Customize the Look and Layout » Customize the layout of other window components
Controls for this application’s view, panels and expand bars are described in the following table. For information that pertains only to views, also see Customize the appearance and layout of views. Task “How To” Show or open a hidden…
When one feature is selected
GenVision Pro Interface » Panels » Details panel » When one feature is selected
If a single feature has been selected in a track in the Overview or Analysis view (e.g., by clicking one time on the feature), the Details panel contains a subset of the following information. Note that the tooltip displayed when you hover over a feature is a subset of…
Save, Close and Exit
Save, Close and Exit
To save one or more sessions: To save one or more sessions or to overwrite a previously saved version of the session in GenVision Pro (.gvp) format To save all open sessions, use File > Save All Sessions or press Ctrl/Cmd+Shift+S. To save only the active…
Jobs panel
GenVision Pro Interface » Panels » Jobs panel
After initiating a sequence match search, you can monitor its progress and download its eventual output from the Jobs panel. This panel is not visible in a project until you have started running at least one search. To open the Jobs panel: Do any of the…
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…
Variants view
GenVision Pro Interface » Views » Variants view
The Variants view shows a table with a row for each variant position and can only be generated for reference-guided assemblies in .assembly format. Depending on which command or tool is used to access the view, the table may contain all variants, filtered variants, or…
Set up local BLAST databases
Search for Sequence Matches » Set up local BLAST databases
In a typical sequence search, this application contacts the BLAST server at the National Center for Biotechnology Information (NCBI) and searches for sequence matches online. But what if your organization bans or limits online searches? Alternatively, what if you want…
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…
Add Data
Add Data
Once you have created a GenVision Pro session, the next step is to add data. GenVision Pro lets you import any combination of SeqMan NGen assemblies, BAM, VCF, and GFF files to a new session or to an existing session that already contains data. The following table…
Welcome screen
GenVision Pro Interface » Welcome screen
The Welcome tab opens when you launch GenVision Pro and can also be launched using the View > Welcome command. This tab is a central location for opening or creating sessions or accessing help. As you open sessions, the Welcome “project” will remain as the…
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 . In the Download Genome…
Structural variation calculation in long-read workflows
Explore Variants and Structural Variations » Explore structural variations » Structural variation calculation in long-read workflows
This topic pertains to the way SeqMan NGen calculates and GenVision Pro displays structural variations (SVs) for long-read data. This information is partially applicable to Illumina MiSeq data as well. As of the Lasergene 17.6 release, SV detection in SeqMan NGen…
Filter the Structural Variation view
Explore Variants and Structural Variations » Explore structural variations » Filter the Structural Variation view
From the Structural Variation view, click the Filter tool () to specify which SVs should appear in the table. A filter dialog appears. All settings in this dialog are optional, and it is fine to leave boxes blank if you do not wish to specify a threshold for that…
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…
Add assemblies
Add Data » Add assemblies
To add one or more SeqMan NGen .assembly packages to the session: Do any of the following: Drag & drop one or more assemblies from your computer’s file explorer onto an open GenVision Pro session. Press the Add assemblies to project button tool…
Numeric tracks (Coverage, Phase consistency)
Work with Tracks » Numeric tracks (Coverage, Phase consistency)
If data is available, you can choose to display a numeric track in the body of the Analysis view. The available numeric tracks are Coverage and Phase consistency. For detailed information about applying tracks, see Work with Tracks. Sources of data for numeric…
Table view
GenVision Pro Interface » Views » Table view
To access the Table view, perform a BLAST search. When the search is complete, the Text and Table views are displayed together in a single popup window that is separate from the main GenVision Pro window. To reopen the views at a later time, click on the Status link in…
Enrichment Report
GenVision Pro Interface » Views » Reports view » Enrichment Report
The Enrichment Report displays exome and gene panel data and is one of several reports available in the Reports views. This report is only available for exome or gene panel assemblies that utilized BED files during the assembly process. To display this report, select…
Alignment tracks
Work with Tracks » Alignment 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 using the method described in Work with Tracks. Briefly, you can display an Alignment track by opening the…
Add BAM and GFF files
Add Data » Add BAM and GFF files
Assemblies made with Geneious, CLC Workbench, BWA, and others are usually output in BAM file format. When you create a templated assembly in SeqMan NGen, the .assembly package output contains the reference sequence(s) as well as feature information and variant calls.…
Choosing and understanding Structural Variation view columns
GenVision Pro Interface » Views » Structural Variation view » Choosing and understanding Structural Variation view columns
To select which columns to display in the Structural Variation view, or to rename or reorder them, click the Choose or rearrange columns () tool. The Choose Columns dialog appears. Available but yet-unused columns are on the left, while currently-applied columns…
Choosing and understanding Variants view columns
GenVision Pro Interface » Views » Variants view » Choosing and understanding Variants view columns
To select which columns to display in the Variants view, or to rename or reorder them, click the Choose or rearrange columns () tool. The Choose Columns dialog appears. Available but yet-unused columns are on the left, while currently-applied columns are on the…
Appendix
Appendix
The Appendix contains the following topics: View a list of supported file types Set preferences for the Internet or for specifying temporary file locations. View IUPAC codes See the installed Lasergene file locations Turn off usage…
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…
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…
Views
GenVision Pro Interface » Views
GenVision Pro views are the large windows on the left of the interface. The following views may be available depending on circumstances. For instance, you may need to select something or perform a search of the BLAST or Entrez databases before a particular view is…
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…
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 >…
Create and analyze variant sets
Explore Variants and Structural Variations » Create and analyze variant sets
When either a single-sample or multi-sample Variants view is active, you can save a selected group of variants as a “set.” This set appears in its own multi-sample Variants view. You can also directly compare two or more variants sets. Create a subset of…
Wrap the Analysis view display
GenVision Pro Interface » Views » Analysis view » Wrap the Analysis view display
To wrap the display in the Analysis view: In the Style panel’s Analysis section, select Automatic wrapping from the Layout drop-down menu. The Analysis view will immediately wrap horizontally. If you had been using a Linear layout and had already split the…
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…
Specify the Experiment or Chromosome to Display
Specify the Experiment or Chromosome to Display
The Genome view can display multiple experiments, chromosomes, contigs or sequences simultaneously. However, only one of these at a time may be displayed in the Analysis view and Overview. To display Genome view rows for all uploaded session data: Do any of the…
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 a subset of the following information: Heading Type of track or assembly name, in blue. Summary – Basic information about what is displayed in…
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…
Search for Sequence Matches
Search for Sequence Matches
This application lets you search National Center for Biotechnology Information (NCBI) databases for matches to text or sequence that you specify. You can also search for sequence matches to a local database. Query part or all of a nucleotide or protein sequence…
Search for sequence matches using BLAST
Search for Sequence Matches » Search for sequence matches using BLAST
The sequence search wizard is used to search a query sequence against one of NCBI’s databases or a previously created local database. The sequence can be part or all of an active sequence, another sequence file on your computer, or typed/pasted-in text. The…
Export
Export
For detailed steps on exporting data and images from GenVision Pro, see the following topics: Export an image of a view (and edit it in PowerPoint) Export data to a file a file}
Search wizard: Job
Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Job
The Job screen is the fourth of four screens in the sequence search wizard, This screen allows you to overwrite the default search name with a custom name and initiate the BLAST search. The text box contains an automatically-generated name for the search job. If…
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…
Add VCF files
Add Data » Add VCF files
A single- or multi-sample VCF file can be annotated and added to a GenVision Pro session as long as you also have the same version reference sequence. Though the workflow takes place within GenVision Pro, the SeqMan NGen wizard is used to set up the job and run it…
Variants tracks
Work with Tracks » Variants tracks
If you are viewing an assembly created in SeqMan NGen, you can add a Variants track to the Analysis view using the method described in Work with Tracks. In contrast to the Alignment track, which lets you see variants at the level of individual bases, the Variants track…
Filter by alignment
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Filter by alignment
The Alignment screen is the one of several screens for filtering a multi-sample Variants view or set, and lets you filter variants in the Variants view based on alignment statistics. Put a check mark next to each type of statistic you wish to filter on, then input…
Explore structural variations
Explore Variants and Structural Variations » Explore structural variations
In addition to variants and small insertions and deletions, genetic variation can also involve large scale rearrangements. These rearrangements may include large insertions and deletions, inversions, and translocations, collectively known as “structural…
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 a subset of the following information: Heading The number of tracks currently selected (in blue). Summary – Description of options available…
Filter by database
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Filter by database
The Database screen is the one of several screens for filtering a multi-sample Variants view or set, and lets you filter variants in the Variants view based on their presence/absence in the dbSNP database and/or their minimum Genomic Evolutionary Rate Profiling (GERP)…
Phase block tracks
Work with Tracks » Phase block tracks
If the session contains phased variant analysis data, a phase block track can be applied to the Analysis view. A phase block track shows quality or confidence score for the phasing calls. The track is a graphical representation of the Phase Block column in the Variants…
Customize the set name and notes
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Customize the set name and notes
The Name screen is the only screen specific to sets when filtering a multi-sample Variants view or set. It is not present when filtering variants that are not part of a set. Initially, the screen contains an automatically generated name with notes describing the…
Variants section
GenVision Pro Interface » Panels » Style panel » Variants section
The Variants section contains options affecting how variants are displayed in the Analysis view when Variants tracks are applied. To access it, click on the expand bar entitled Variants in the Style panel, or choose View > Style > Variants. Most of this section…
Analysis section
GenVision Pro Interface » Panels » Style panel » Analysis section
The Analysis section contains options affecting the wrapping style for rows in the Analysis view. To access it, click on the Style panel expand bar entitled Analysis, or choose View > Style > Analysis. The following table shows tasks that can be performed using…
Search wizard: Options
Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Options
The Options screen is the third of four screens in the sequence search wizard, and has two tabs: Selection and Matches. These tabs allow you to customize miscellaneous parameters relating to the BLAST search. Click the Selection tab to make it active. In the…
Search wizard: Search
Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Search
The Search screen is the second of four screens in the sequence search wizard. The Search screen is used to choose the BLAST program, as well as whether you wish to search an online database or within a locally-stored database. Choose whether you want to search…
Filter by impact
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Filter by impact
The Impact screen is the one of several screens for filtering a multi-sample Variants view or set. This screen lets you filter variants in the Variants view based on the functional impact of the variants and/or presence inside or outside splice sites. Check or…
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…
Text view
GenVision Pro Interface » Views » Text view
To access the Text view, perform a BLAST search. When the search is complete, the Text and Table views are displayed in a popup window that is separate from the main GenVision Pro window. To reopen the views at a later time, click on the Status link in the Jobs panel.…
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 >…
Filter by type
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Filter by type
The Type screen is one of several screens for filtering a multi-sample Variants view or set, and is used to specify type and size thresholds that variants must meet to appear in the Variants view, as well as to specify whether you wish to only include variants from…
Change the Analysis view color scheme
GenVision Pro Interface » Views » Analysis view » Change the Analysis view color scheme
The foreground and background color schemes for the Analysis view are specified in the Analysis section of the Style panel. To open the section, click on the expand bar entitled Analysis, or choose View > Style > Analysis. Each available color scheme is described…
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…
Chromosomes section
GenVision Pro Interface » Panels » Explorer panel » Chromosomes section
The Chromosomes section shows a table of chromosomes in the currently-selected experiment and allows you to easily maneuver between chromosomes in a multiple sample project. To access this section, click on the Explorer tab on the right and expand the Chromosomes…
When multiple sequences are selected
GenVision Pro Interface » Panels » Details panel » When multiple sequences are selected
If multiple sequences have been selected in the Genome view, the Details panel contains a subset of the following information: Heading Number of sequences currently selected, in blue. Sequence type – DNA or RNA (if known). Min./Max.…
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…
Rename Experiments, Tracks, or Chromosomes
Rename Experiments, Tracks, or Chromosomes
A selected experiment (e.g. assembly), track, or chromosome can be renamed manually or by using specified data fields. See the following topics for details: Rename a single experiment, track, or chromosome Rename tracks or chromosomes automatically using…
Style panel
GenVision Pro Interface » Panels » Style panel
The Style panel lets you customize view formatting and layout. To open this panel, do any of the following: Click on the Style tab (). Use the View > Style > Style command. Right-click within a view and choose Show Style Panel. To change settings in the…
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…
Set preferences
Appendix » Set preferences
To open the Set Preferences dialog on Macintosh, choose GenVision Pro > Preferences (macOS 12 and lower) or GenVision Pro > Settings (macOS 13 and higher). On Windows, choose Edit > Preferences. GenVision Pro has four types of preferences that can be…
Try It! – Analyze an E. coli assembly
GenVision Pro Tutorials » Try It! – Analyze an E. coli assembly
The following tutorial uses free data from the DNASTAR website to demonstrate a typical workflow in GenVision Pro. The tutorial is in four parts, which should be done in order. Begin with Part A: Start a new session and rename a sequence using data…
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 BED or Wiggle files
Add Data » Add BED or Wiggle files
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…
Filter sequence search results
Search for Sequence Matches » Search for sequence matches using BLAST » Filter sequence search results
When you press the Filter results tool () in the header above the Table or Pairwise views, there are two options: Filter and Clear Filter. Clicking on the Filter option opens the following dialog: Use the drop-down menu to choose a filter type, then enter the…
Reports view
GenVision Pro Interface » Views » Reports view
The Reports view consists of two separate reports, each displaying data related to a single assembly or other data source. To display the Reports view, select a row in the Experiments section of the Explorer panel and click the Show Reports () tool or use the View >…
Filter by experiment
Explore Variants and Structural Variations » Compare variants across samples » Filter a multi-sample Variants view or set » Filter by experiment
The Experiment screen is the first of several screens for filtering a multi-sample Variants view or set, and is where you choose the experiments and comparison baselines used to filter variants in the Variants view or in a variant set. The Experiment wizard screen is…
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…