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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 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…
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 BLAST 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 you…
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…
Change the default application for opening files
Create or Open a Session » Open an existing session » Change the default application for opening files
Windows 7 and Windows 8: 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…
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 BLAST 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 BLAST Search wizard. The Search screen is used to choose the BLAST program and database. Specify whether you wish to search for Nucleotides or Proteins. Select the desired BLAST program from the Using…
Genome view
GenVision Pro Interface » Views » Genome view
The Genome view can display multiple experiments, chromosomes, contigs or sequences simultaneously. To access the Genome view, do any of the following: Press the Home () button tool. Use the View > Genome > Show command. Click on the Genome tab. Use…
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…
Add sequences
Add Data » Add sequences
You can add a sequence to the session if it is in any of the following formats: sequence file (.seq), SeqBuilder Pro format (.sbd), MegAlign Pro format (.msa), Genbank (.gbk) or FASTA (.fas and _.fasta). To add sequences: Do any of the following: Drag & drop one…
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…
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…
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…
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…
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…
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…
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…
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…
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…
Search wizard: Query
Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Query
The Query screen is the first of four screens in the sequence search wizard. The Query screen is where you add the query sequence, i.e., the sequence for which you wish to locate matches in the NCBI BLAST database. At the top of the screen, next to “Search…
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…
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…
Find a Location
Find a Location
Navigate to a specific position in the sequence: To move the cursor to a specific point on the sequence, do any of the following: Use the navigation tools in the main GenVision Pro header. Open the Places panel and double-click on a previously-stored…